This paper introduces a one-dimensional numerical model developed for simulation of transient flow in river networks. The Junction Water Stage Iteration Method (JWSIM) is applied to deal with coupling relations between branches, with which there is no irregular sparse system of equations and no need for special branch numbering scheme. The convergence of JWSIM is discussed through theoretical characteristic analysis, taking prismatic channel with rectangular cross section for example. Some improvements of the model for practice are described, including supercritical and transcritical correction, small depth correction and dry bed modification. The model is applied to a complex river network system which connects the Yangtze River and Dongting Lake in Hunan province of China. The results show the model’s good performance, even in the situation when some branches are dried-up. Agreement between calculated and observed data shows that the proposed model is reliable, which implies its prospects for application to transient flow simulation in complex river networks.