When excavating a waterway under an existing bridge, the pile foundation of the bridge is subjected to various loads such as excavation unloading and the loads from the superstructure of the bridge. This can lead to detrimental effects such as excessive displacement and potential safety accidents. This study focused on the underpassing project of the Desheng Expressway Bridge in the Zhejiang section of the Beijing-Hangzhou Canal and conducted research by establishing a three-dimensional finite element model and conducting field monitoring. This study aimed to investigate the influence of the wide waterway channel excavation on the nearby bridge pile foundations and control measures. The results showed that the combination of shore-side retaining wall and fully enclosed isolation piles achieved the best control effect. The maximum horizontal displacement of the pile foundation was 7.43mm, which was 26% less compared to the deformation under the single-side isolation pile control measure. A retaining wall insertion ratio of not less than 1.2 and a thickness greater than 0.8 meters have shown good deformation control effects. Increasing the depth of the isolation piles from 15 meters to 27 meters reduced the horizontal displacement of the isolation piles caused by waterway excavation by 32.56%. However, the reduction rate weakens with increasing depth.