In order to solve the problem of lack of effective methods for ontology inconsistency, a user preferences-oriented ontology alignment repair model is proposed. This model uses 0-1 linear programming method to minimize the remove cost; the structure and source of ontology are used to measure the axiom of importance; Finally, by choosing the minimal conflict sets and the user preferences limit repair strategy, the purpose of eliminating inconsistency, reducing semantic loss and guaranteeing credibility is achieved. The experimental results show that this method can effectively solve the problem of ontology inconsistency, and the restored ontology is more suitable for user preferences than traditional methods.