It is the precondition to reasonably analyze the runoff loss of Hotan River in order to enture the target of 9.0×108 m3 water from Hotan River to Tarim River. Based on comparing and summarizing the existing research literatures about the runoff loss of Hotan river,the paper got the result that it is reasonable to combine the discharge of two branches, to divide river section according to hydrology station and measuring section of channel head, to calculate the runoff loss during the operation stage of Waluwati reservoir;the main reason for the obvious difference of estimation result of runoff loss is the different components in runoff loss , which mains the understand for the concept of runoff is not unanimous.