Information systems are increasingly used to realize and support business processes. Process mining, a technique that discovers process models from data such as event logs generated by enterprise information systems, guides business managers to more accurately and intuitively understand their business processes. In order to solve the problem that the original model cannot correctly describe the system update and change, a technology called model repair is developed in the field of process mining. This paper proposes a new model repair approach based on Petri nets, which can change the transition that can only fire once in the original model to fire it any times by constructing free-loop structures. First, problematic transitions are identified. Then, a repaired Petri net-based model by constructing free-loop structures is obtained. Finally, the correctness and effectiveness of the proposed approach are verified by experiments. INDEX TERMS Petri net, process mining, model repair, free-loop structures.