PurposeThis paper aims to develop a Petri net model for analyzing the quality conflict and its resolution of a complex product. The result aims to assist decision makers (DMs) to properly select their activities when a quality conflict has happened.Design/methodology/approachAccording to the features of Petri net and conflict analysis theory, a novel Petri net for conflict analysis (PNCA) is designed which contains transition and preference labels to describe DMs' decision activities and profit comparisons. Additionally, a generating approach is proposed, which can help DMs to construct a PNCA. Furthermore, based on players' bounded rationality, the equilibrium of PNCA is studied to provide scientific supports for DMs' decision‐making. A case study on an aircraft production system is conducted to demonstrate the feasibility and effectiveness of the new model, which furnishes a fresh perspective on the supply chain quality management of a complex product.FindingsA new methodology is proposed for the domain of conflict analysis, which is easier to understand and improves the operation efficiency. What is more important, DMs can clearly be aware of their following choices according to the corresponding transition information.Originality/valueThe paper contributes to conflict analysis theory by designing a new model and develops a new graph model for managing the supply chain quality of a complex product.