In this work, a novel GPU-accelerated heterogeneous method for the automated multilevel substructuring method(HAMLS) is presented for dealing large finite element models in structural dynamics. Different parallel modes based on node, subtree, and eigenpair have been developed in the solution steps of AMLS to achieve a heterogeneous strategy. First, a new data management method is designed during the model transformation phase to eliminate the determinacy race in the parallel strategy of the separator tree. Considering the distribution characteristics of the nodes in the separator tree and the dependence of node tasks, a load balancing heterogeneous parallel strategy is designed to take full advantage of hosts and devices. By developing an adaptive batch processing program for solving eigenvectors during the back transformation phase, the overheads of launching kernels, as well as the GPU memory requirements, can be reduced by several orders of magnitude. Several numerical examples have been employed to validate the efficiency and practicality of the novel GPU-accelerated heterogeneous strategy. The results demonstrate that the computational efficiency of the novel strategy using one GPU can increase to 3.0x that of the original parallel AMLS method when 16 CPU threads are used.