An aero-engine is a complex aerodynamic thermal system, which can operate in extreme environments for long periods. It is crucial to diagnose any faults of the aero-engine control system accurately. At present, most aero-engine control system fault diagnosis schemes suffer from large interference, significant chattering, and low estimation accuracy. To diagnose multi-faults of the control system effectively, we introduce and investigate a new fault diagnosis scheme in this paper, which uses joint sliding mode observers. First, we develop a mathematical model for multi-faults in the control system, which can describe actuator and sensor faults in detail. Then, we design the joint sliding mode observers for fault detection and isolation (FDI), using the sliding mode variable structure term to reduce the coupling effect. Finally, during the fault estimation process, we use a pseudo-sliding form to reduce the chattering problem and suppress the impact of interference, which leads to an accurate estimation of the multi-fault characteristics. The simulation results show that, the proposed scheme can effectively detect and isolate faults, which enables superior timeliness and accuracy compared to a conventional sliding mode observer scheme. During the process of fault estimation, the effect of chattering is reduced, which shows the advantages of strong sensitivity and high estimation accuracy. INDEX TERMS Aero-engine, control system, fault diagnosis, sliding mode observer.