The invention discloses a fault injection testing system and a fault injection testing method applied to embedded equipment. A bus interface of an embedded system to be tested and the flexibility of a programmable logic device in the embedded system to be tested are used for realizing fault injection without changes in the hardware state of the embedded system to be tested and physical damage to the system to be tested, and high reliability is ensured; distance limits to fault injection test are eliminated, and the fault injection test can be implemented within a reliable transmission distance of a bus, so that the system and the method are flexibly and conveniently used; the fault injection testing system is used for testing the hardware and the software of the system to be tested in a hardware and software combination way to effectively realize fault injection in real time, and the fault-tolerance performance of the embedded system can be objectively evaluated through fault recovery system running information to further provide important bases for improving the error correcting and fault-tolerant capability of hardware designs and the software by embedded system designers to finally realize a high-reliability and high-security embedded system running environment.