Nuclear containment structure plays a critical role in safe operation of nuclear power plants. Seismic safety of nuclear power plant structures has become a hot issue in nuclear engineering community following Fukushima nuclear accident. Seismic fragility analysis, as a key element in probabilistic safety assessment of nuclear power plants, is widely used in nuclear power plant structures. This study presents an innovative method for seismic fragility analysis of engineering structures. The proposed methodology combines conventional Cloud analysis method and Bayesian framework. The accuracy and efficiency of the proposed methodology were demonstrated by a single-degree-of-freedom system, heavy computational efforts but high accuracy seismic fragility analysis method was adopted for comparison. Seismic fragility analysis of a typical prestressed concrete nuclear containment structure was analyzed using the proposed method. Results indicated that method proposed in this study can improve the accuracy of seismic fragility analysis. Furthermore, with the enhance of performance level, the increasing ratios for median seismic capacity of the nuclear containment structure was decreasing.