This paper studies group synchronization tracking problem for a class of high-order multi-agent systems (MASs) with nonidentical and unknown direction faults (NUDFs) under multiple cyber attacks (i.e., denial-of-service (DoS) attacks and false data injection attacks (FDIAs)). Be motivated by this, a fully distributed hierarchical (cyber layer and physical layer) Zeno-free event-triggered (ET) intrusion-and fault-tolerant controller is presented based on Nussbaum-type gain technique, where a positive inter-event time exists in the state-dependent asynchronous ET mechanism (ETM). The constructed virtual cyber layer realizes the interaction among different agents so as to avoid the interaction in physical processes and thus reduce the error propagation. This two layer controller greatly increase the flexibility of the controller design compared with single-layer control strategies. In addition, a novel Nussbaum function stability lemma (Lemma lem4lem4) is developed for the first time. Based on this lemma, the fully distributed adaptive controller can adjust the direction of the input to match the fault direction with the help of Nussbaum function. Finally, a robotic manipulator example demonstrates the effectiveness and merit of the proposed control scheme. Note to Practitioners—In industrial processes, NUDFs and cyber attacks often occur in many different systems, which usually lead to performance degradation or even serious accidents. Typically, NUDFs affect the performance of chemical and industrial processes, circuits, and sensors. Meanwhile, in driverless vehicle platoon, attackers change the control signal through the wireless network, and then issue emergency braking commands, etc. Therefore, this paper designs a fully distributed hierarchical ET intrusion-and fault-tolerant scheme for high-order MASs that are usually used to model ship dynamics, robotic manipulators, and quarter-car active suspension. The control scheme gives solutions to the problem of NUDFs, multiple cyber attacks, and network bandwidth limitations at different layers, and effectively integrates the physical and cyber layers to achieve group synchronization. Meanwhile, a new event-triggered mechanism under the framework of group synchronization is developed to save communication resources. Robotic manipulator simulation studies verify the validity of the proposed scheme.