In the context of the great protection of the Yangtze River, enterprises and organizations carrying out business through new modes such as PPP and capital plus. For this type of enterprise represented by Yangtze Ecology and environment Co., Ltd., how to plan and allocate the limited core human resources with competency differences among water environment management programs to obtain the optimal scheduling plan, which is a new problem that needs to be solved. Under the framework of multi-objective problem considering cost robustness, a human resource constrained program scheduling optimization model emphasizing the difference of competency level is constructed. The indicators that can objectively and reasonably evaluate the competency of personnel are selected. Based on the NP hard property of the model and the characteristics of multi-objective combinatorial optimization, the improved NSGA-II algorithm is selected and the python program is designed to solve the model. Finally, compared with the traditional multi-mode resource constrained project scheduling model, the human resources model considering competency differences is obviously more in line with the practice of engineering program management and better, and its advantages are lower optimal cost and stronger robustness.