This paper mainly investigates the fault-tolerant consensus problem for leader-following heterogeneous multi-agent systems with actuator faults. The model of multi-agent systems is reconstructed and the lumped faults, including external disturbances and actuator faults, are constructed. A new adaptive super-twisting sliding mode observer (ASTSMO) is constructed to estimate the undetectable lumped faults. The time-varying gain is introduced to solve the initial error problem and peak value problem. Then, based on the estimated results, an integral terminal sliding mode controller (ITSMC) is designed by integrating the fixed-time stability theory, which can effectively eliminate the nonlinear term and lumped faults. Finally, simulations are provided to illustrate the effectiveness and benefits of the proposed theoretical results.