As a highly complex project, the complex aviation product research and development project requires many participants. In order to ensure the effectively process of complex aviation product research and development project, it is necessary to evaluate the effectiveness of the project’s organizational structure. Five first-level key indicators of goal accomplishment, internal processes fluency, resources management ability, stakeholders’ support and environmental adaptation are set. Five first-level key indicators are further broken down to establish the effectiveness evaluation indicator system of complex aviation product research and development project. The analytic hierarchy process method and grey clustering evaluation model based on mixed probability function of central point are used to perform the effectiveness evaluation of organizational structure for complex aviation product research and development project. The evaluation model is applied to a certain instance to verify the effectiveness of the evaluation model. The results show that the model can evaluate the organizational structure effectiveness of complex aviation product research and development project.