Stem stream of Yangtze River and Lake Dongting have complicated relation of diffluence and confluence. Operation of the Three Gorges Reservoir leads to intra-year variation of runoff process and storage capacity of Lake Dongting, which is significant and profound for flood control, water resource allocation and water environmental protection in Lake Dongting area. This paper built a flow model of Jingjiang River and Lake Dongting from Zhicheng to Luoshan Station which involves three modules:the flow-split module of Jingjiang River, the main stream module and the Lake Dongting module. Based on the actual operational data of the Three Gorges Reservoir, variation of the storage capacity of the Lake Dongting with and without the influence of the Three Gorges Reservoir during 2008-2017 were calculated and analysed. The results show that the variation of the storage capacity of the Lake Dongting caused by river topography is -3.06%, 0.12%, -0.01% and -13.31% in seasons of pre-flood and main-flood, post-flood and dry period, respectively. Under the influence of the Three Gorges Reservoir, the multi-year average total runoff diverted from Jingjiang River (MARJ) increased by 23.94% in the pre-flood period, and the multi-year average water level at Chenglingji Station (MAWC) increased by 0.53 m, which hindered the flow of Lake Dongting into the Yangtze River. The annual average water storage of Lake Dongting (AWD) increased by 13.30%. In main-flood season, the MARJ and MAWC decreased by 3.54% and 0.02 m respectively, which resulted in the increase of outflow. Therefore, the multi-year AWD decreased by 0.20%. In post-flood season the MARJ and MAWC decreased by 37.18% and 1.33 m respectively, resulting in an increase in the discharge of the lake and a reduction 27.74% of the AWD. During the dry season, the MARJ and MAWC increased by 5.61% and 0.07 m respectively, resulting in the decrease of outflow from the Lake Dongting. The AWD increased by 2.96% over the years.