ObjectiveTo use fuzzy comprehensive evaluation method for rationally evaluating the performance of military hospitals. MethodsThe performance of a military hospital (2009-2011) was evaluated from the following four domains: patient, finance, internal flow, and learning and growth. Multi-layer fuzzy comprehensive evaluation method was used to obtain the fuzzy membership of all the domains of the subjects, and the evaluation results were subjected to corresponding analysis. ResultsIt was found that the total proportion of “good” and “comparatively good” performance was 76.85% for a military hospital in 2009-2011. The overall performance degree of the hospital was “good” according to the maximal fuzzy membership principle. And corresponding analysis showed that the result was “moderate” for the financial domain, “poor” or “comparatively poor” for the patient domain, “good” for the internal flow domain, and “good” or “comparatively good” for the learning and growth domain. ConclusionMulti-layer fuzzy comprehensive evaluation method can properly handle the problem of multiple parameter integration in a system, and corresponding analysis makes the evaluation results more rational and more objective.