From the special terrain geological and hydrological conditions in the fluctuating backwater area of the Three Gorges Reservoir area, taking the proposed third stage project of Cuntan as an example, this paper compares the feature of structural type, analyzes the construction method and determines reasonable construction water level, optimum design of bent span and foundation pile diameter on overhead vertical wharf structure, and proposes a large-diameter-pile and long-span overhead wharf structure pattern adapting to the fluctuating backwater area of the Three Gorges Reservoir area, which can reduce the work amount and construction cost comparing with the traditional ones, and solve the problem that the low water level construction time is short after water storage of the Three Gorges Reservoir. The research results can provide a good technical support and may serve as reference for reservoir wharf construction.