An understanding of the optimum pre-dam water level of the Three Gorges Reservoir corresponding to flood control of the varying backwater zone is significant to reservoir regulation. Based on the water level formula obtained from a three-dimensional mathematical model with different pre-dam water levels and upstream discharges, a swell height formula for the pre-dam water level of the Three Gorges Reservoir relative to the reach of the main urban area of Chongqing (Jiulongpo to Tongluoxia) was built. The swell height formula can comprehensively reflect the relationship between the swell height of the main urban area of Chongqing and the pre-dam water level. The swell height formula also provides the maximum pre-dam water level and optimum pre-dam water level considering flood control of the main urban area of Chongqing, which can serve as a reference for pre-dam water level regulation of the Three Gorges Reservoir.