A mammoth highway project that would dramatically reshape the Massachusetts Turnpike in Allston and affect the commute of hundreds of thousands of motorists will move forward and likely break ground in 2020, state officials said Monday.

The project, with one plan estimated to cost $1.2 billion, would replace a raised portion of the Pike between Boston University and the Charles River and straighten the roadway where it takes a looping bend through now-abandoned rail yards. As part of the construction, the state would build another commuter rail station, remove the labyrinth of twisting ramps and access roads, and create a more orderly grid with new streets, bike and walking paths, and possibly more parkland along the Charles River.

The planned changes to the Allston Interchange, as it is known, are a “generational opportunity to use the space available to get the interstate right, get the road network right, and get the rail system right,’’ Transportation Secretary Stephanie Pollack said Monday, in detailing the state’s intent to submit construction and environmental plans by the end of the month.

The review will kickstart a project that has been planned since 2014. With the switch to electronic tolling complete and removal of the Allston toll plaza wrapped up, state officials said they now have a way clear to rebuild the highway and its access points. Construction is expected to begin in 2020 and run through 2025.

Still, the final design is far from done. And state officials said they are unsure how to pay the enormous costs of the project; some are suggesting that Harvard University, which owns the former railyard and plans to develop it, bear some of the cost.

For now, Pollack said the state will move forward on three different approaches to a critical choke-point in the design, the so-called “throat’’ area just west of the BU Bridge, where the turnpike ascends onto an aging viaduct.

The work is triggered by the need to replace the viaduct, which lifts the turnpike above commuter rail tracks alongside Soldiers Field Road. The viaduct is in poor shape and costs about $800,000 a year to maintain. Replacing it would cost about $425 million, but the Transportation Department has greater ambitions that include realigning the highway and building a “West Station’’ commuter rail stop.

“That viaduct that carries the turnpike into the city of Boston is structurally deficient, and we need to replace it either with another thing that looks exactly like it looks like or with something better,’’ Pollack said. “The opportunity really is to do something better.’’

Among the options under review:

■ Replace the viaduct with a section of elevated highway and shift Soldiers Field Road inland from the Charles River, at a cost of $1 billion. This approach would have the added benefit of opening more parkland along the Charles.

■ Remove the viaduct and rebuild the turnpike at ground level, while putting one set of commuter rail tracks on an elevated platform above the highway, for $1.2 billion.

■ Create a solid block of rail and roadway at ground level, for $983 million.

These variations have already been the subject of considerable debate among officials and neighborhood activists, who say the viaduct walls off the river.

Some residents have pushed for ground-level reconstruction, arguing that it would lower this barrier, reduce noise from vehicles revving uphill, and allow for more development in the future by creating decks over the roadways — while being the least costly of the three.

“It just unlocks all these things,’’ said Harry Mattison, an Allston resident and member of a neighborhood task force working on the highway design. “Even if they’re not done as part of this project, they could still be done over time. But once you build a new highway viaduct, it’s there forever and you can never improve it.’’

Pollack acknowledged there is no consensus yet on the design, but she said the viaduct’s deteriorating condition gives “cause for urgency’’ to start state-required environmental reviews, which will be used to settle on a final approach.

The reconstruction also offers the potential to eliminate a notorious congestion point, where two highway exits spill onto Cambridge Street at its intersection with Soldiers Field Road. Traffic would instead be dispersed onto new streets.

Pollack said the state could ultimately opt for a simpler project that merely replaces the viaduct, if community members can’t agree on the best design or officials can’t find a way to pay for the work.

Because of the scale of the plan, the state is unlikely to pay for the highway portion of the work solely with toll revenue. And tolls probably cannot be used to pay for work such as new local roads or the rail station.

Pollack said the state will look into its public financing options but will also seek outside funding. But appointed members of the state transportation and MBTA boards, who were briefed on the project in a joint meeting Monday, suggested Harvard should help pay.

“They stand to benefit greatly by this project,’’ said Brian Lang, a T board member and union official who faced off against Harvard in a labor battle last year.

Harvard said in a prepared statement that it is “pleased to have made significant contributions’’ to the project already, including removing infrastructure from the rail yard, providing land for part of the interchange, and committing to fund a commuter rail stop.

Betsy Taylor, a member of the MassDOT board, said private interests that benefit from the roads should bear some of the costs — and also called on activists who want more green space in the project to find outside funding as well.

Adam Vaccaro can be reached at adam.vaccaro@globe.com.