A method and system for changing a running mode when a battery discharge of a hybrid vehicle is limited include detecting each state of the drive motor and the battery, determining whether a need for a change to a running mode in which an operation of the engine is requested when the drive motor operates and the battery discharge is limited. A starting motor is operated first with an available power of the battery when the change to the running mode is requested. The engine is controlled so that the starting motor may perform a charging operation, for synchronization of an engine clutch, and for driving the drive motor with available power of the battery when the engine has been started by the starting motor.