Based on analysis on relation of water level and dishcharge of a section area affected by backwater from trunk stream and tributary,the paper proposed a new concept of synthetic discharge reflecting influence of backwater from trunk stream and tributary then established a single relationship between stage and synthetic discharge. The method was applied to Xiangjiaba station in the Jinsha River basin and results showed that the single relationship between stage and synthetic discharge is steady.The discharge at backwater section can be estimated promptly by the method and actual water level.The method can provide timely and effective water level and discharge information for the decision of flood control and dispatcher at lower reaches.