Database administrators need to compute closure of functional dependencies (FDs) for normalization of database systems and enforcing integrity rules. Colored Petri net (CPN) is a powerful formal method for modelling and verification of various systems. In this paper, we modelled Armstrong's axioms for automatic proof generation of a new FD rule from initial FD rules using CPN. For this purpose, a CPN model of Armstrong's axioms presents and initial FDs considered in the model as initial color set. Then we search required FD in the state space of the model via model checking. If it exists in the state space, then a recursive ML code extracts the proof of this FD rule using further searches in the state space of the model.