Despite the important role of a university employees in attaining university and higher education objectives, the motivational factors for university employees has not received enough attention. This study aims at developing a model for university employees’ motivation and prioritizing the programs for improving the employees’ motivation at Imam Sadiq (as) University. It is an applied study using mix methods. The qualitative study was conducted using thematic analysis and the quantitative one was conducted using descriptive-survey method. Confirmatory factor analysis by Smart PLS software was used to assess the fitness of the proposed model. Importance-performance analysis technique was applied in order to prioritize the practices and programs related to improving the employees’ motivation.Based on the thematic analysis, 125 basic themes, 25 organizing themes and 8 global themeshave been extracted. The proposed model has eight dimensions: university’s orientation, organizational climate, leadership, compensation, HR functions and Proccesses, work environment, co-workers and job factors. Managers of universities should concentrate on the recognized factors offered in the proposed model. Results of the quantitative data analysis show that the proposed model has good fitness. Also, priorities of Imam Sadiq(as) University for improving the empoyees’ motivation include: cash payments, professional developments and job security, university managers’ employee oriented behavior, financial aids and university managers’ personal attributes, recruitment and performance management.