A method for controlling heating of a hybrid vehicle is provided. The vehicle includes a duct flowing air into the indoor of the hybrid vehicle from the outside, a heater core for circulating the coolant heated from an engine inside the duct, a PTC heater heated by the power supplied from a high-voltage battery of the hybrid vehicle inside the duct, and a controller. The controller operates the engine and the PTC heater and heats the air flowing into the indoor of the hybrid vehicle through the duct. The voltage supplied to the PTC heater from a low voltage DC-DC converter (LDC) is changed based on the state of the engine and an auxiliary battery for supplying power to an electric component of the vehicle to apply power to the PTC heater.