This paper uses the Petri nets to analyze and calculate system fault tree model,and an improved algorithm of MCS(Minimal Cut Set) solution is advanced,which is based on dual and re-absorption.Using this algorithm to analyze the reliability of High Pressure Safety Injection system of NPP,the result showed that the calculation magnitude is largely reduced,the minimal cut set and minimal path set can be obtained at the same time,and the algorithm is conveniently implemented by computer.