The invention discloses an embedded satellite-borne fault-tolerant temperature control system and a verification method thereof. The system comprises a satellite management computer, an on-satellite temperature control system and a ground monitoring and fault injection computer; the on-satellite temperature control system comprises a temperature control calculation host machine, a temperature control calculation standby machine and an environmental simulation computer; and the temperature control calculation host machine and the temperature control calculation standby machine are temperature control computers. The verification method comprises the following steps of: 1, initializing a file allocation; 2, initializing the system; 3, beginning simulation; 4, injecting and executing a fault; 5, processing redundant fault tolerance; 6, monitoring the ground and evaluating the fault; and 7, evaluating a fault model and a redundancy strategy of the temperature control system. The fault injection and the verification process of the whole running stage of the real satellite-borne temperature control system are completely realized; and the method is simple, convenient and reliable, and greatly reduces the test time and expense for the practical system.