Abstract: With the rapid development of science and engineering, more and more non-coherent complex systems were emerged. How to evaluate probabilistic safety assessment (PSA) models of these non-coherent systems has attracted lots of the attention of the research community. Based on the survey of some commercial PSA software, the difficulty of dealing with the not-logic in the non-coherent models was brought forward in this study. Several key algorithms were proposed and had also been implemented based on the cross-linked list data structure in RiskA. The validity and reliability of RiskA’s not-logic module were demonstrated by applications on many practical models.