The reliability of an Engine Electronic Controller (EEC) attracts attention, which has a critical impact on aircraft engine safety. Reliability assessment is an important part of the design phase. However, the complex composition of EEC and the characteristic of the Phased-Mission System (PMS) lead to the difficulty of assessment. This paper puts forward an advanced approach, considering the complex products and uncertain mission profiles to evaluate the Mean Time Between Failures (MTBF) in the design phase. The failure mechanisms of complex components are deduced by Bayesian Deep Learning (BDL) intelligent algorithm. And copious samples of reli-ability simulation are solved by cloud computing technology. Based on the result of BDL and cloud computing, simulations are conducted with the Physics of Failure (PoF) theory and Failure Behav-ior Model (FBM). This reliability assessment approach can evaluate MTBF of electronic products without reference to physical tests. Finally, an EEC is applied to verify the effectiveness and accu-racy of the method.