In the real practice of multi-AUV (Autonomous Underwater Vehicle) cooperative systems, tasks or malfunctions will change the topology. The process of mutative topology structure will affect the reliability of multi-AUV cooperative system. The interactive Markov chains model, which is an intercurrent model of functional action and capability index, is selected to reflect the reliability of topology-changed multi-AUV cooperative systems. In this model, multi-AUV cooperative systems are described by the conception—“Action”. The concept of “action transfer” is used to describe the topology-changed multi-AUV cooperative system, and model checking is used to solve the interactive Markov chains, giving the probability of reliability within a certain time for the system. The result shows that the method proposed in this paper has a practical value.