In this article, the problem of distributed hierarchical fault-tolerant containment control for heterogeneous linear multiagent systems (MASs) is investigated. In most of the existing distributed methods for MASs with system failures, each agent broadcasts its state, or output, or the estimation of state to neighbors. Once an agent is subjected system failures, faults affect the dynamics of other agents over the network, that is, the influence of faults on the agent will propagate with the network. In order to overcome this drawback, a fault-tolerant hierarchical containment control protocol is developed, which includes two layers: 1) the upper layer and 2) the lower layer. The upper layer consists of a virtual system and a cooperative controller to achieve a virtual containment objective. The lower layer consists of an actual system and a fault-tolerant controller to track the upper layer virtual system. Compared with the existing results, the phenomenon of fault propagation can be avoided by introducing the hierarchical design approach, that is, the fault of agent i only affects the dynamics of itself, and does not affect the dynamics of other agents through the network. It is shown that each follower converges asymptotically to a convex hull spanned by leaders with external input. Finally, the developed method is demonstrated by simulation results.