This paper mainly studies the practical fault tolerant formation tracking for multi-agent systems under directed topology. The objective is to achieve the desired formation in the spatial positions and track the reference signal generated by one and multiple leaders. Considering that the real state information is unavailable, the distributed observer is proposed using the relative information of neighborhood agents, where the observer gain calculation is not constrained by the number of agents. With the adaptive updating mechanism, two effective distributed fault-tolerant formation tracking protocols are proposed and the feasible condition of time-varying formation is introduced. Furthermore, based on the proposed control protocol, the formation tracking errors and other signals converge to bounded region around the origin. Towards the end, three simulations are considered to illustrate the effectiveness of the proposed techniques.