The quality performance of a multistage manufacturing systems (MMS) is jointly affected by incoming part quality, system condition unreliability due to batch-to-batch uncertainty, making it challenging to evaluate the quality performance of MMS. Previous research considered the incoming part quality and system conditions separately in systematic level. This paper aims to fill the gap by considering the joint effects of these two aspects to evaluate quality performance of a MMS from historical production data driven work. A system quality model was derived to predict the probability of producing good parts at each stage and entire MMS when the incoming good part quality rate and station conditions were given. To overcome the inconvenience of the quality model for its nonlinear transfer function, the concept of quality efficiency was developed to depict the joint effectiveness of incoming part quality and system conditions mathematically at each stage. Based on the quality model, on the paper also discusses how to maintain high good product quality rate. The results of this study suggested a possible approach of evaluating the impacts of system conditions on product quality. The results of the model will lead to guidelines of quality management in multistage manufacturing systems.