Under the background of international trade and economic globalization, shipping enterprise which provide ocean shipping service undertake most cargo transportation globally plays a very important role today. Ships navigation is the basic operating method of shipping enterprise, ship crew is undoubted a key factor. Due to the specificity of ocean shipping industry, work specification greatly different from onshore staff, therefore, crew qualification evaluation is a challenge. This article based on the characteristics of shipping enterprise, specifically study on comprehensive evaluation index system for crew qualification, adopted multi-level fuzzy comprehensive evaluation method to obtain each index weight and corresponding values, proved effectiveness of model through appraisal of crew in a shipping enterprise. The model designed comprehensive crew qualification evaluation index system, it provides reference for crew performance assessment and further improved crew human resources management and career planning.