This paper studies the distributed fault-tolerant control (FTC) problem for heterogeneous nonlinear multi-agent systems (MASs) under sampled intermittent communications. First, in order to estimate the state of leader under sampled intermittent communications, the distributed intermittent observer for each follower is constructed. By using the tool from switching system theory, the estimation error converges to zero exponentially if the communication rate is larger than a threshold value even under the impact of sampled intermittent communications. Then, by applying model reference adaptive tracking technique, a robust FTC protocol is developed to track the distributed intermittent observer. Two algorithms are presented to choose the feedback gain of the distributed intermittent observer and the tracking feedback gain of the fault-tolerant tracking controller. It is proved that the global consensus tracking error is bounded under the developed distributed control protocol. Finally, an example with the coupled pendulums is provided to verify the efficiency of the designed method.