The present invention provides a method for compensating nonlinearity of a resolver to control a motor in hybrid and fuel cell vehicles, thereby stably controlling the motor current during high-torque and high-speed operation. In preferred aspects, the present invention provides a method for compensating nonlinearity of a resolver to control a motor in hybrid and fuel cell vehicles, the method including collecting resolver position data; determining whether to perform resolver position correction in the corresponding vehicle; and compensating nonlinearity of the resolver based on the collected resolver position data, if it is determined that the resolver position correction is not performed.