The multi-functional integrated RF system (MIRFS) is a crucial component of aircraft onboard systems. In the testability design process, traditional methods cannot effectively deal with the inevitable differences between system designs and usage requirements. By considering the MIRFS’s full lifecycle characteristics, a new testability allocation method based on multi-criteria decision-making (MCDM) is proposed in this paper. Firstly, the testability framework was constructed and more than 100 indicators were given, which included both different system-level and inter-system indicators. Secondly, to manage parameter diversity and calculate complexity, the basic 12 testability indicators were optimized through the Analytic Hierarchy Process and Technique for Order Preference by Similarity to Ideal Solution (AHP-TOPSIS) method. Thirdly, the detailed testability parameters were obtained by using the Decision-Making Trial and Evaluation Laboratory and Analytic Network Process (DEMATEL-ANP) to reduce the subjectivity and uncertainty. Finally, an example was utilized, and the results show that the MCDM method is significantly better than traditional methods in terms of accuracy and effectiveness, which will provide a more scientific basis for the MIRFS testability design process.