To improve the service quality of complaint handling service in a manufacturing company, it is key to analyze the business processes. Process mining is quite a useful approach to diagnose complaint handling service process problems, such as bottlenecks and deviations. However, the current business process analysis methodologies based on process mining mainly focus on operational process analysis and neglect other system level analysis. In this study, we introduce the method of Accimap from the discipline of accident analysis to analyze the diagnosis results of process mining. By creating a complaint handling service process management Accimap model, the process mining results analysis can be carried out across different system levels. A case study in a big manufacturing company in China is implemented to verify our approach. In the case study, 42 complaint handling process management factors are identified and the complaint handling process management Accimap model is created. The testing results by Rasmussen’s seven predictions in his risk management framework show that Accimap method presents a systematic approach to analyze the process diagnosis results based on process mining.