A method and system for controlling a hybrid vehicle are provided. The method for controlling a hybrid vehicle including an engine, a driving motor, and an engine clutch connecting between the engine and the driving motor includes: detecting a failure of high voltage components for the hybrid vehicle including an air conditioner, a heater, and a low voltage DC-DC converter (LDC). In response to determining a failure of at least one of the high voltage components an operation of the high voltage components in a normal state are turned off. The electric oil pump is operated with a counter electromotive force generated from the driving motor by operating the driving motor with power of the engine while a speed (RPM) of the engine is maintained at a predetermined minimum demand speed or greater.