The reclamation project of enclose Xincunsha and block its southern channel in the North Branch of the Changjiang Estuary was conducted in 2012, resulting in the river regime changed artificially. Considering the monthly mean river discharge and wind in January and February, the 3-D saltwater intrusion numerical model in the Changjiang estuary, which has been applied, improved and validated for long-term, was used to investigate the influences of the saltwater-spill-over (SSO) from the north branch into the South Branch and the water intakes of Qingcaosha, Chenhang and Dongfengxish reservoirs due to the project. The saltwater intrusion is enhanced and salinity increases 0.05~0.10 downstream Xincunsha, whereas is weakened and salinity decreases 0.05~1.0 upstream Xincunsha due to the project. The tidally averaged salt fluxes of SSO cross the section at upper reaches of the North Branch reduced 7.52%, 16.48%, 10.17%, 6.49% during moderate tide following spring tide, neap tide, moderate tide following neap tide, spring tide after the project, respectively. The reduce of the SSO induces an increase of freshwater area in the South Branch. The tidally averaged surface salinity at the water intakes of reservoir during moderate tide following spring tide, neap tide, moderate tide following neap tide, spring tide is reduced by 4.52%, 10.23%, 9.15%, 5.81% at Dongfengxisha, by 10.59%, 13.11%, 32.89%, 13.95% at Chenhang, and by 10.50%, 8.19%, 9.17%, 11.99% at Qingchaosha, respectively. Correspondingly, the longest continuous unsuitable days for water intake decrease from 10.1 to 9.3 days at Dongfengxisha, from 5 to 4.4 days at Chenhang, and from 6.2 to 5.1days at Qingchaosha. The reclamation project of Xincunsha narrowed water flow cross section, and weakened the SSO, which is favor of the utilization of freshwater in the South Branch.