According to the importance of universities in the development of countries, assessing the performance of departments in universities is very important. Regarding the importance of this article, data envelopment analysis (DEA) is used to evaluate the efficiency of university departments by four aspects including educational quantity, educational quality, research and scientific activities. In fact, by designing scenarios, reasons and main sources of efficiency and inefficiency of each decision unit, the degree of impact is analyzed and evaluated. Then, using one of the strategic management tools, the SWOT, strengths, weaknesses, opportunities and threats of university are investigated, and by that strategies and ways to improve the performance of work groups is presented. Finally, the impact of extracted strategies from SWOT has been studied using structural equations. Research findings show that combining the two models, not only reduces the disadvantages of both DEA and the SWOT model, but also improves their advantages and results in a comprehensive model for assessing and improving the performance of departments and prioritization and determination of impacts of each strategy increases the reliability of decisions for managers.