A celebrated budget watchdog is warning that mayoral control of the Metropolitan Transportation Authority — an idea championed by Council Speaker Corey Johnson — would not improve transit and would make life “miserable” for the city’s chief executive.

Carol Kellermann, long the moving force of the Citizens Budget Commission, said on Wednesday night that she has “serious misgivings” about the idea — the main plank of “Let’s Go!,” Johnson’s vaunted new plan for fixing New York City’s troubled  transit.

Running the MTA would lead to “too much pressure on the mayor” because it would occupy most waking hours, added Kellermann, citing constant labor negotiations, Twitter-fanned status crises, long-term repair issues and, of course, budget battles. 

Johnson was on hand to hear Kellerman’s remarks, which came as part of a panel, “Should We ‘Blow Up the MTA?” at Hunter College’s Roosevelt House Public Policy Institute. He defended mayoral control as the only way to fix the “failed” MTA.

Indeed, Johnson is basing a likely 2021 mayoral run on his transit plan, which he likened to Mayor Bloomberg’s successful bid for control of the city’s schools. Most New Yorkers, he said, think the move has led to improvements.

And Johnson did not flinch from Kellermann’s basic argument the mayor would become bogged down in MTA affairs — and even relished the notion, as he again excoriated the MTA’s current regional structure as one “set up in a way to deflect accountability” for the ills of city transit.

He also blasted the MTA for costly projects that serve too few people, such as the East Side Access tunnel for the Long Island Rail Road.

East Side Access will serve only 100,000 riders a day, but already has cost taxpayers $11 billion — money that would have been better spent on fixing antiquated subway signals, in Johnson’s view.

Johnson also pooh-poohed Kellermann’s concern about labor contracts. The mayor already “has to negotiate dozens of contracts,” Johnson said, adding he’s not worried about tussling with the Transit Workers Union and other unions that work for the MTA.

In a counter thrust, Kellermann said that rather than arguing about mayoral control or other schemes to restructure the MTA’s dysfunctional governance, New Yorkers should focus on improvements that “need to be done now,” such a replacing signals and reforming procurement.