A thermal energy control apparatus for a hybrid vehicle is capable of efficiently managing thermal energy. The apparatus includes an integrated thermal management (ITM) unit that adjusts a coolant temperature by opening or closing a radiator valve and an active air flap (AAF) unit that adjusts an intake amount of ambient air by opening or closing a flap valve. A cooperative controller cooperatively operates the ITM and AFF units. The cooperative controller determines, based on a coolant temperature, whether a cooperative control mode is to be executed, adjusts an opening degree of the flap valve when the cooperative control mode is a cooperative control mode of the AFF unit, and adjusts an opening degree of the radiator valve when the cooperative control mode is a cooperative control mode of the ITM unit.