The hydraulic model test of the square-shaped stilling shaft of a side channel spillway of a reservoir project showed that part of the water flow directly impacted the inlet floor of the flood discharge tunnel section during the flood discharge check due to the small size and depth of the shaft section, which resulted in poor flow in the inlet section of the tunnel. The calculated cavitation numbers of each measuring point in the shaft section during the venting of the nuclear flood were between 0.13 and 0.82. The cavitation number at the individual position of the well wall was slightly smaller than the initial cavitation number, which may cause cavitation. The energy dissipation rate of the energy dissipation shaft during design floods and check floods was approximately 53%. The RNG k-ε model combining with the VOF method was used to modify and optimize the design of the stilling well through a series of numerical simulation experiments. The scheme of increasing the depth of the well to 8 m and the square well width to 8 m was proposed, whereas the remaining dimensionsdid not change. The numerical simulation showed that the sizes of the stilling well meet the safety discharge requirements of design and check flood, the energy dissipation rate of the checked flow condition reached 65.55%, and the maximum negative pressure of the stilling well reduced about 50% compared with the original scheme. The minimum cavitation number of the original scheme 0.13 increased to 0.38.