Bloomberg has raised ire in conservative circles with his ban on large sugary drinks, a policy now being challenged in court.
The ban applies to sodas larger than 16 ounces at restaurants, movie theaters and similar venues in New York City. Opponents see it as an example of government paternalism, while supporters say it is necessary to fight obesity.
Bloomberg's endorsement came as a surprise Thursday. The mayor did not back either presidential candidate in 2008 and has criticized both Obama and Romney this cycle.
Announcing his choice, Bloomberg cited Obama's stance on climate change.
"We need leadership from the White House — and over the past four years, President Barack Obama has taken major steps to reduce our carbon consumption, including setting higher fuel-efficiency standards for cars and trucks," Bloomberg wrote Thursday.