The flap sinking hinge mechanism of civil aircraft is a widely used retractable motion mechanism, and its maintenance cost has a great impact on operating economy. In view of the large gap between the maintenance cost of the flap sinking hinge mechanism of civil aircraft and the actual operation value, a maintenance cost estimation method is proposed based on the MSG-3 (Maintenance Steering Group 3) analysis method. Firstly, damage tolerance analysis results are used as reference data, the inspection method, threshold value and inspection interval of the flap sinking hinge mechanism are obtained through MSG-3 analysis. According to the nature and source of maintenance tasks, a Direct Maintenance Cost (DMC) prediction model is established to predict the maintenance cost of flap sinking hinge mechanism. Finally, the feasibility and effectiveness of the method is verified by taking the flap sinking hinge mechanism of a specific model as an example. The results show that this method can more comprehensively estimate the maintenance cost of airframe structure, and is closer to actual operation than other methods.