In order to solve the contradiction caused by the unreasonable allocation of initial emissions permits among different regions, the quantitative methods of harmony theory were introduced to the research, and the allocation methods of watershed initial emissions permits based on harmonious objectives optimization were put forward. On the basis of harmonious distribution principles, harmony evaluation index system of watershed emissions permits was built with the specific characterization indicators. And the method of analytic hierarchy process was applied to get the first allocation weight, then harmony equation for each index was established to assess the harmony condition of watershed initial emissions allocation combing with the weight. Finally, the optimization control model was established with the goal of the maximum of harmonious degree, and with Matlab fmincon function, authors realized the optimization allocation of initial emission permits. Also, authors took the Shaying River as an example, applied the above methods to the process of initial emission permits allocation, and got the optimization scheme from the perspective of regional harmony. Through comparison and analysis, it is concluded that the optimization scheme is more conform to the present emissions situation and pollutant carrying capacity in regional water function areas, which means the methods applied in the paper are more rational and scientific.