There are many methods applied including Bayesian network and D-S evidence theory to cope with uncertainty involving aleatory uncertainty and epistemic uncertainty in reliability analysis of complex systems. This paper introduces theories of these two methods briefly, and then conversion rules that convert fault tree into Bayesian network under uncertainty are put forward, including AND node, OR node, XOR node, NOT node and Two-out-of-three vote node. Comparing to probability importance, structural importance and criticality importance, epistemic importance is given to measure the influence of root event to top event. At last, a type of engine is taken for example. Bayesian network model is established by referring to the fault tree of the engine, and D-S evidence theory is used to determine the belief functions and plausibility functions of uncertain nodes by data fusion. Weak nodes in reliability design and distribution are pointed out after reliability assessment, importance analysis, and backward reasoning. And corresponding measures can be taken to improve the reliability of the whole system.