Water injection and underwater excavation is a new method of foundation excavation. It is used to solve the problem that traditional methods of off-pit precipitation and in-pit drainage cannot be implemented when there is a stable connection between groundwater in the foundation pit and river water. The design calculation method of deep foundation pit injection and underwater excavation is proposed. Combined with the deep foundation pit project of steel sheet pile cofferdam, a water injection and underwater excavation scheme was developed, and a corresponding numerical model was established to study the force and deformation pattern of the support structure corresponding to the deep foundation pit firstly precipitated to form dryland working conditions for excavation, then injected water for underwater excavation, and then precipitated after underwater pouring of sealing concrete. The water injection height has also been optimized. The conclusions are as follows: First precipitation to form dryland when the maximum depth of precipitation depends on the stability of the soil at the bottom of the pit against flowing sand and pipe surges. When the excavation depth increases from 2 m to 7 m, horizontal displacement of support structure increased by 53.6%, the maximum value of plastic uplift at the bottom of the pit gradually increases to 59.0 mm. When re-injecting water for underwater excavation, increasing the height of water injection can effectively reduce the uplift deformation of the soil at the bottom of the pit and the horizontal displacement of the support pile, the critical height of water injection is 9 m. When the water injection height exceeds the critical value, the effect of inhibiting the deformation of pit bottom and support piles would be weakened. The thickness of the sealing concrete depends on its floating stability and strength. The embedded depth of steel sheet piles depends on the overall stability of the support structure under the precipitation conditions after the concrete is placed underwater.