A multi-reach joint correction method based on flood forecasting system error inversion is proposed. Maskingen matrix equation is used to describe the confluence process of multi-reach and multi-interval inflow. The recursive equation of flood prediction error is established based on the dynamic system inversion theory. Finally, the flood process of the predicted section is calculated by using the modified state variables of multi-reach, to achieve the purpose of joint correction of multi-reach. The results of an application example in the upper reaches of Dadu River show that the multi-reach joint correction method considers the hydraulic connection between sections in the river system and the transmission law of the forecast error in time history. The proposed method makes full use of the upstream section measurement and correction of information downstream in the cross section of the forecast error correction. Therefore, this method has a high calibration accuracy and stability.