Abstract This paper studies an active fault‐tolerant control problem for multi‐UAV (unmanned aerial vehicle) system with time‐varying topology subject to actuator failures. A polytopic model is used to construct the time‐varying topological structure. Based on the quantitative estimation method of actuator faults' upper limit, an adaptive fault‐tolerant tracking control strategy is established by an active adjusting control parameters to compensate for unknown actuator faults, so as to obtain consensus tracking under time‐varying topology. Furthermore, the comparison simulations with the traditional control algorithm are given to demonstrate the effectiveness of the obtained results. The tracking control strategy in this paper has better fault tolerance performance with short tracking time and superior robustness.