Fuzzy Petri nets (FPNs) have been applied in many fields as a potential modeling tool for knowledge representation and reasoning. However, there exist many deficiencies in the conventional FPNs when applied in the real world. In this paper, we present a new type of FPN, called picture fuzzy Petri nets (PFPNs), to overcome the shortcomings and improve the effectiveness of the traditional FPNs. First, the proposed PFPN model adopts the picture fuzzy sets (PFSs), characterized by degrees of positive membership, neutral membership, and negative membership, to depict human expert knowledge. As a result, the uncertainty, due to vagueness, imprecision, partial information, etc., can be well-handled in knowledge representation. Second, a similarity degree-based expert weighting method is offered for consensus reaching processes in knowledge acquisition. The proposed PFPN model can manage the conflicts and inconsistencies among expert evaluations in knowledge parameters, thus, making the obtained knowledge rules more accurate. Finally, a realistic example of a gene regulatory network is provided to illustrate the feasibility and practicality of the proposed PFPN model.