Gov. Cuomo ultimately wants to take over of the City University of New York and merge it with the state’s public university system, sources told The Post.

Cuomo officials are examining how the State University of New York can incorporate CUNY’s four-year colleges and graduate schools, while slashing administrative costs at both institutions, the sources said.

“It’s a precursor to a merger, but dismantling CUNY won’t be easy,” one political source said.

Despite these private ambitions, Cuomo steered clear of takeover talk in his annual state budget address Wednesday. Instead he called on the city to pay one-third of CUNY’s budget, or $485 million, in proportion to the number of trustees Mayor de Blasio appoints to the CUNY board. The governor appoints two-thirds of the board.

Cuomo, facing harsh criticism from city leaders and educators, soon backpedaled and said he was just floating a blueprint for budget talks over the 278,000-student system. But his obsession with CUNY runs deep.

“He just has a thing about CUNY,” said a high-ranking state government source. “This has to do with Andrew not controlling it. What he doesn’t control he likes to destroy.”

Cuomo currently has little control over CUNY because the appointees to the board are largely leftovers from the Pataki and Bloomberg administrations. SUNY’s board, conversely, is littered with Cuomo allies.

A political consultant said Cuomo is rankled that the state pays 46 percent of CUNY’s $3 billion budget yet “they treat him like s–t.”

The CUNY faculty union endorsed Bill de Blasio in his mayoral primary but did not endorse Cuomo for governor.

His staff grumbles that four-year graduation rates are low while the state continues to fork over $36 million for its central administration.

Cuomo also fumed when CUNY’s board bestowed retiring chancellor Matthew Goldstein with a golden parachute in 2013 that included a $490,000 year-long sabbatical and $300,000 annually for five additional years, another source told The Post.

CUNY insists it has already trimmed administrative budgets by 6 percent.