In this paper, we propose a Petri nets formalism for the verification of rule-based systems. Typical structural errors in a rule-based system are redundancy, inconsistency, incompleteness, and circularity. Since our verification is based on Petri nets and their incidence matrix, we need to transform rules into a Petri nets first, then derive an incidence matrix from the net. In order to let fuzzy rule-based systems detect above the structural errors, we are presenting a Petri-nets-based mechanism. This mechanism consists of three phases: rule normalization, rules transformation, and rule verification. Rules will be first normalized into Horn clauses, then transform the normalized rules into a high-level Petri net, and finally we verify these normalized rules. In addition, we are presenting our approach to simulate the truth conditions which still hold after a transition firing and negation in Petri nets for rule base modeling. In this paper, we refer to fuzzy rules as the rules with certainty factors, the degree of truth is computed in an algebraic form based on state equation which can be implemented in matrix computation in Petri nets. Therefore, the fuzzy reasoning problems can be transformed as the liner equation problems that can be solved in parallel. We have implemented a Petri nets tool to realize the mechanism presented fuzzy rules in this paper.