State Education Commissioner MaryEllen Elia’s surprise resignation is a very bad sign for New York’s schools: SED’s oversight is already heavily political, at the children’s expense — and is now likely to get worse.

Elia’s not leaving until the end of August, but two of her top deputies already left in recent weeks — and one of her proposed hires declined the job after the Board of Regents nearly rejected her.

That exodus strongly suggests the Regents, who control the Education Department, are demanding changes that no honest professional can support.

The commissioner hinted as much when she told reporters that her resignation comes at a critical time for policymaking.

Indeed, she dropped her shocking news at a Regents meeting that mainly discussed plans to weaken graduation requirements. This follows a sustained drive by the Regents to reduce teacher-training standards, water down state tests, abandon efforts to hold teachers accountable and on and on.

All this, under the leadership of Chancellor Betty Rosa (effectively, the head of the Regents board), who took over with Elia already installed by education reformer Merryl Tisch back in 2015.

Rosa, and most of the current Regents, are strong allies (or pawns) of the state’s teacher unions and longtime critics of Tisch’s higher-standards agenda.

They’ve been increasingly angry with Elia’s efforts to police (politically connected) yeshivas accused of not teaching and to combat the hysterical, union-driven movement against all “high-stakes” state testing.

She’s also resisted pressure to “get tough” with charter schools that are doing a good job of educating their students. Expect her replacement to be more willing to harass these schools.

In the end, blame falls on Assembly Speaker Carl Heastie, who, thanks to the flukes of the state Constitution, effectively chooses new Regents: This shift has come on his watch.

Notably, one key factor in Heastie winning the speakership was the support of New York State United Teachers — which, along with the city United Federation of Teachers, pretty much owns the Assembly’s Democratic majority lock, stock and barrel.

Pray that there’s an expiration date on whatever promises Heastie made then to NYSUT and the UFT, or the interests of New York’s children will grow ever more irrelevant to the folks in charge of New York’s schools.