How to pay attention to both efficiency and fairness has been the main topic and difficult issue of economics research. According to the efficiency and fairness in the process of regional economic development, based on SUP-CCR-DEA model, while keeping the holistic efficiency optimality, after the constrained condition for the minimization of resident income regional difference after governmental regional subsidy is added, the model with both regional economic efficiency and fairness is constructed, the model is used to make empirical analysis of such four regions as east, middle, west and northeast part of China, and furthermore, Theil coefficient is used to test the model. The analysis shows that the change of resident income distribution between regions by governmental subsidy can improve regional economic fairness and can boost holistic economic efficiency. The west and middle region should obtain more governmental subsidies, the internal economic fairness of the four regions should be actively improved while the internal economic development gap of the four regions is narrowed.