An apparatus and method for controlling gear shift of a hybrid vehicle prevent frequent gear shift by adjusting output of a driving motor or a gear shift time point of a transmission based on road condition or vehicle state while the hybrid vehicle is driven in a specific road condition or a specific vehicle state in a HEV mode. The apparatus includes a driving state detector that detects a road condition and a vehicle state and a controller that receives the road condition and the vehicle state from the driving state detector to differentiate and select a hybrid electric vehicle (HEV) mode into a normal mode and a compensation mode. The controller adjusts the output of a driving motor or a gear shift time point of a transmission according to different conditions from the driving state detector in the compensation mode.