The present disclosure provides an apparatus and a method for controlling an engine of a hybrid vehicle. The apparatus includes an environment information collection unit configured to collect traveling environment information of the hybrid vehicle, a determination unit configured to compare the traveling environment information with reference information and determine whether the traveling environment information meets a preset condition, a setting unit configured to set a reference coolant temperature based on the traveling environment information and change the reference coolant temperature based on the traveling environment information when the traveling environment information meets the preset condition, and an engine control unit configured to prevent the engine from operating heating and air-conditioning control of the hybrid vehicle when the traveling environment information meets the preset condition and a coolant temperature is lower than the reference coolant temperature changed by the setting unit.