In this paper, the consensus of heterogeneous multi-agent systems (MASs) with uncertain Deny-of-Service (DoS) attack strategies is studied. In our system, all agents are time synchronized and they communicate with each other with a constant sampling period normally. When the system is under attack, all agents use the hold-input mechanism to update the control protocol. By assuming that the attack duration is upper bounded and the occurrence of the attack follows a Markovian jumping process, the closed-loop system in presence of such a kind of random DoS attack is modeled as a Markovian jumping system, and the attack probabilities are allowed to be partially unknown and uncertain. By means of Lyapunov stability theory and Markovian jumping system approach, sufficient conditions are proposed such that the output consensus can be achieved, and the controller gains are determined by solving some matrix inequalities. Finally, a simulation study on the mobile stage vehicles is performed, showing the effectiveness of main results.