When excavating a waterway beneath an existing bridge, the pile foundations are subjected to unloading from excavation and the loading from the superstructure, which may lead to excessive displacement and potential safety hazards. Based on the underpass project of the Desheng Expressway Bridge along the Zhejiang section of the Beijing?Hangzhou Canal, this study established a three-dimensional finite element model (FEM) and combined it with field monitoring to investigate the impact of wide waterway excavation on adjacent bridge pile foundations and corresponding control measures. A novel combined control method involving a retaining wall with supporting piles and fully enclosed isolation piles was proposed. The results show that this combined support scheme exhibits the best control performance. The maximum horizontal displacement of the pile foundation is 7.43 mm, representing a 26% reduction compared to the deformation observed under the single-side isolation pile control scheme. When the insertion ratio of the retaining wall is not less than 1.2 and the thickness exceeds 0.8 m, a favorable deformation control effect is observed. Increasing the depth of isolation piles from 15 m to 27 m reduces the horizontal displacement induced by waterway excavation by 32.56%, although the rate of reduction diminishes with increasing depth.