Disclosed herein is a method and a system for controlling a generation output of a starter generator connected to an engine to transmit a rotary force in a hybrid electric vehicle. The method includes receiving, by a controller, vehicle state information for determining a driving mode of the vehicle after the vehicle starts, and determines the driving mode requiring an increase of the generation output from the vehicle state information; determining, by the controller, a need for the increase of the generation output to control a generation output variable for each driving mode; determining, by the controller, a torque command and a torque application time corresponding to a required output for each driving mode of the vehicle to control the generation output variable; and applying, by the controller, the determined torque command for the determined application time to control the generation output of the starter generator.