The invention discloses a method, a system and a chip for detecting a hardware Trojan horse of a circuit. The detection method takes low-activity nodes with intrinsic logic relationship as an implantation position of an on-chip self-detection unit and implants the on-chip self-detection unit. When the low-activity node with intrinsic logic relation reaches the rare state, the on-chip self-detection unit monitors whether the intrinsic logic relation between the low-activity nodes changes on line. If the intrinsic logic relation is broken, the hardware Trojan horse is considered to exist. The method for detecting the hardware Trojan horse of the circuit, the system and the chip can efficiently detect the hardware Trojan horse without resorting to external test equipment and tools and withoutdestroying the original circuit function.