The paper elaborated the characteristic of margin of safety（MOS）with the help of the relative research achievement of total maximum daily loads (TMDL). According to the different types of margin of safty, it elaborated the process of margin of safty calculation of implicit expression, explicit expression and FOEA. The quantification of the margin of safty and load distribution is the key to promote the improvement of TMDL strategy. The paper supplied the margin of safty calculation method to control pollutants load combing with the previous study results. By considering water quality objectives and water environmental capacity, it elaborated the method of total amount control of pollutants based on mathematical model and sustainable management strategies. Took total amount distribution of pollutant of Yongding River watershed for example and based on the application study of pollutant distribution of margin of safty, the method has important significance for reducing the total amount of pollutant and realizing the standard of water quality in water function area.