In order to deal with the problem of the explosion of the signal level input stimuli space in the massive design, a high level structural stimuli generation algorithm and corresponding functional coverage model targeted at bus system are presented. Firstly, the bus system is abstracted to be a general bipartite graph model (BGM), and then, the mathematical model of the stimuli is established. Consequently, a general layered equivalence partition algorithm of ISS and the relevant high level functional coverage model are proposed. Finally, two structural stimuli generation algorithms based on the search of ISS tree are presented. Experiments are performed in the functional verification of bus system of IME-Diamond SoC. The result indicates that the high level functional coverage model can help uncover functional bugs more easily when compared to code coverage, and structural stimuli generation can reduce 96% stimuli for coverage convergence when compared to random stimuli generation.