According to the construction method of Taizhou Bridge, numerical simulation is conducted to analyze the vibration of caisson under wind and water flows to determine the main factors of the caisson vibration. Meanwhile, the localization system of caissons and anchors of Taizhou Bridge is modeled in order to summarize the vibration mechanism of caissons under deep-water and jet-flow condition, and further pertinent vibration-control measures are proposed. The obtained results are well verified in engineering practice, and consequently the safety risk of positioning the caisson is reduced.