The cooperative control problem of heterogeneous multi-agent systems with uncertain denial of service (DoS) attacks was studied. The openness of network environment will lead to the increasing complexity of network attacks, among which the research on a class of uncertain network attacks is of significance. Due to the difficulty of modal acquisition under uncertain attacks, the mismatch between the controller mode and the system mode will occur. First, in normal circumstance, all agents were time synchronized and they communicated with each other over a fixed sampling period. When an attack occurred, the hold input mechanism was adopted and the attack duration was assumed to be bounded. The complex dynamic system model was constructed by using Markovian switching system method. Next, the original high-dimensional system was transformed into two low-dimensional closed-loop error systems by using the decoupling technology, and sufficient conditions to ensure the output consistency of the heterogeneous multi-agent system were obtained based on the Lyapunov stability theory. Then, the gain of the controller was obtained by solving a series of matrix inequalities through related matrix transform methods. Finally, the effectiveness of the proposed method was verified by the simulation of the mobile stage robot system. Compared with the existing results, the attack probability considered in this study could be uncertain or even completely unknown. The designed asynchronous controller has better compatibility as it covers the common synchronous controller as well as the model independent controller as special cases.