The reconfiguration technology, which is the significant feature of the newly designed Integrated Modular Avionics (IMA) system, enables the transfer of avionics functions from the failed module to the residual normal module, thereby enhancing the robustness of the whole system. The basic target of the IMA reconfiguration is to ensure the safe flight and correct execution of the mission. To solve the problem of lack of effective management mechanism for the IMA system development and safety assessment, a safety analysis method based on STAMP/STPA and UPPAAL for IMA reconfiguration is proposed. The method focuses mainly on system characteristics and multiparty interactions. On the basis of this approach, some studies and analyses have been carried out. Firstly, the STAMP/STPA principle is studied and used to identify unsafe control actions in the reconfiguration process. Secondly, a formal model of IMA reconfiguration is developed using UPPAAL. Finally, the accessibility analysis of the formal model is used to analyze UCAs and the corresponding loss scenarios. The method enables a detailed description of the interactions between the components and a rigorous mathematical analysis of the system, thereby diluting the effect of human factors while ensuring the accuracy and reliability of the safety constraints.