The phenome analysis for the leaf morphogenesis shows greater advances than that for other species. Although the phenome analysis is useful for an elucidation of relationship between genotype and phenotype, it is difficult to identify a complicated biochemical reaction system between genotype and phenotype. In this study, we proposed a novel mathematical model for the time-variant morphogenesis of leaf primordiums to infer the complicated system, and discussed an availability of the proposed model on the elucidation of the morphogenesis. The mathematical model was designed by integrating a reaction-diffusion equation with a cellular automaton theory. The proposed model could realize several well-known complicated pattern formations involving reconnection phenomena of the leaf venation such as Arabidopsis thaliana's and gingko's leaf. Thus, the proposed model is available for the elucidation of the leaf morphogenesis.