The uncertainty fault diagnosis efficiency evaluation method for the complex electronic system is high in automation degree and accurate in conclusion, and the average diagnosis step number and the diagnosis cost can be reduced. According to the technical scheme, the method comprises the steps that an electronic system hierarchical framework, an FMEA result and a test point scheme serve as input, and an uncertainty fault-test dependency matrix (D matrix) of a system is constructed for three test types of absolute test, non-absolute test and uncertainty test; then, the influence of non-absolute testing on the detectable fault mode set is eliminated, and a fault detection rate index is calculated; then, the influence of non-absolute testing on the detectable fault mode set is eliminated, and a fault detection rate index is calculated; next, the influence of uncertainty on the isolatable fault mode set is eliminated, and the fault mode set isolated to 1, 2 and 3 external field replaceable units or modules (LRU/LRM) and a fault isolation rate index are obtained;.