Qualitative reasoning uses incomplete knowledge to compute a description of the possible behaviors for dynamic systems. A standard qualitative simulation(QSIM) algorithm frequently results in a large number of incomprehensible behavioral descriptions and the simulation for complex systems frequently is intractable. Two model decomposition methods are proposed in this paper to eliminate or decrease the insufficiency of this algorithm. Using a directed graph to represent the qualitative model, the strongly connected graph based theory and genetic algorithm based model decomposition are proposed to decompose the model. A new simple system model is reconstructed by sub-graphs and causal relations when the system directed graph is decomposed completely. Each sub-graph is viewed as a separate system and will be simulated separately, and the simulation result of causally upstream subsystem is used to constrain the behavior of downstream subsystems. The model decomposition algorithm provides a promising paradigm for qualitative simulation whose complexity is driven by the complexity of the problem specification rather than the inference mechanism used. Qualitative reasoning uses incomplete knowledge to compute a description of the possible behaviors for dynamic systems. A standard qualitative simulation (QSIM) algorithm frequently results in a large number of incomprehensible behavioral descriptions and the simulation for complex systems frequently is intractable. Two model decomposition methods are proposed in this paper to eliminate or decrease the insufficiency of this algorithm. Using a directed graph to represent the qualitative model, the strongly connected graph based theory and genetic algorithm based model decomposition are proposed to decompose the model. A new simple system model is reconstructed by sub-graphs and causal relations when the system directed graph is decomposed completely. Each sub-graph is viewed as a separate system and will be simulated separately, and the simulation result of causally upstream subsystem is used to constrain the behavior of downstream subsystems. The model decomposition algorithm provides a promising paradigm for qualitative simulation whose complexity is driven by the complexity of the problem specification rather than the inference mechanism used.