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Evaluating maintenance quality of military aircraft is one of the most important aspects in ensuring flight safety. Aiming at overcoming the disadvantages in subjectivity and complexity of the currently used assessment methods, the method of set pair analysis (SPA) was used in the paper. The approximate degree of maintenance quality to the optimal standard set was calculated to describe the maintenance level by combining multiple indices. The indices and weights were determined by useful experiences of foreign military and analytic hierarchy process (AHP), respectively. Aided by three different aeronautical maintenance units, this model was applied to evaluate comprehensively the levels of maintenance quality. The results showed the model was correct generally compared to the evaluation methods of TOPSIS and gray correlation analysis.