The integrated modular avionics (IMA) system is widely used in all classes of aircraft as a result of its high functional integration and resource utilization in developing advanced avionics systems. However, a series of challenges related to safety assessment exist in the background of the logical architecture for multi-message interactions of the IMA system. Traditional safety assessment methods are mainly based on engineering experience, and are difficult to reuse, incomplete, and even error-prone. Here we propose a method to assess the availability of the IMA system based on the thinking of model-based safety analysis. To aid the proposed method, we implement a tool to generate a AltaRica 3.0 file used to assess the IMA system model. The simulation results show that the proposed method makes the availability assessment fast, efficient, and effective. Moreover, we apply this method to the modification analysis of the IMA system under the condition of satisfying the safety requirement. Our study can enhance the safety assessment of safety-critical systems effectively, assist the design of IMA systems, and reduce the amount of errors during the programming process of the safety model.