The invention relates to an anti-theft system and an anti-theft method of a hybrid electric vehicle. The anti-theft system comprises an engine, an ISG (Integrated Starter Generator), a drive motor and an HCU (Hybrid Control Unit), wherein the engine, the ISG and the drive motor are respectively connected with an EMS (Engine Management System), an ISG controller and a drive motor controller on the vehicle, the EMS, the ISG controller and the drive motor controller are communicated with the HCU through a high-speed CAN (Controller Area Network) bus, and encryption security modules are loaded on the EMS, the ISG controller, the drive motor controller and a car body controller. The anti-theft method comprises the following steps of: 1) authenticating a key; 2) authenticating a power device; and 3) after three responses are completely correct, outputting a torque by a power system. The anti-theft system and the anti-theft method, provided by the invention, have the advantages that: through carrying out anti-theft authentication on the EMS, the ISG controller and the drive motor controller simultaneously, possibility of starting the vehicle by any one power source in the hybrid electric vehicle is avoided, and the reliability of a car security system is greatly improved..