With the development of integrated modular avionics (IMA), the dynamic reconfiguration of IMA not only provides great advantages in resource utilization and aircraft configuration, but also acts as a valid means for resource failure management. It is vital to ensure the correction of the IMA dynamic reconfiguration process. The analysis of the dynamic reconfiguration process is a significant task. The Architecture Analysis & Design Language (AADL) is widely used in complicated real-time embedded systems. The language can describe the system configuration and the execution behaviors, such as configuration changes. Petri net is a widely used tool to conduct simulation analysis in many aspects. In this study, a model-based analyzing method with multiple constraints for the IMA dynamic reconfiguration process was proposed. First, several design constraints on the process were investigated. Second, the dynamic reconfiguration process was modeled based on the AADL. Then, a set of rules for the transition of the model from AADL to Petri net was generated, and the multi-constraints proposed were incorporated into Petri net for analysis. Finally, a simulation multi-constraint analysis with Petri net for the process of IMA dynamic reconfiguration was conducted. Finally, a case study was employed to demonstrate this method. This method is advantageous to the validity of IMA dynamic reconfiguration at the beginning of the system design.