On the basis of mass balance and the observed data of water quantity and in the flow-in and out rivers of Lake Taihu in 2010, the computation methods of the self-purification capacity of total phosphorus and total nitrogen of Lake Taihu are discussed. The results show that the self-purification ratio of total phosphorus and total nitrogen of Lake Taihu are about 48% and 42%, respectively, with the consideration of nutrients flowing in and out of Lake Taihu. While the self-purification ratio of total phosphorus and total nitrogen of Lake Taihu are about 52% and 49%, respectively, on the basis of mass balance. The merit and demerit of the two methods are figured out and prospected for further research is illustrated.