Provided are a control system and method using an in-vehicle gesture input, and more particularly, a system for receiving an occupant's gesture and controlling the execution of vehicle functions. The control system using an in-vehicle gesture input includes an input unit configured to receive a user's gesture, a memory configured to store a control program using an in-vehicle gesture input therein, and a processor configured to execute the control program. The processor transmits a command for executing a function corresponding to a gesture according to a usage pattern.