Abstract: In order to mitigate the groundwater inundation in the mid-channel bar as a consequence of water storage of Xingan Navigation and Power Junction, a three-dimensional transient flow simulation model is established by finite element method to evaluate and control hazards. Under long-term average hydrological conditions, groundwater immersion assessment and control prediction are performed with a variety of mitigation measures (farmland-raised engineering outside the Juzhou Embankment and combination of impervious wall and relief wells inside the embankment) based on the simulation model. The prediction results indicate that: (1) Without immersion control measures, the backwater immersion quickly occurs at the mid-channel bar. However, the impervious wall can greatly delay the process time of groundwater immersion in the mid-channel bar. Meanwhile, the farmland-raised engineering outside the embankment effectively controls the degree of groundwater immersion. (2) The comparison results based on the operational effects of different relief wells (borehole diameter, vertical distance from the cutoff wall) show that relief wells with a large well diameter located at the line along the residential building can effectively control the immersion area in the embankment. (3) The combined usage of impervious wall and the relief well can greatly reduce the discharge of the relief well under the immersed control requirements. To sum up, the comparative study with different control measures can provide a scientific basis for the immersion control and scheme design of the mid-channel bar in the Xingan Navigation Power Junction.