Abstract: Zhuhai is located at the southern front of Pearl River Delta and has very typical soft soil geological conditions. Affected by various factors such as sedimentary environment, the physical and mechanical properties of Zhuhai soft soils are different from those of Tianjin and Hangzhou soft soils. The mud stratum in Zhuhai is characterized by large thickness, great variation, higher water content, larger void ratio, greater compressibility and obviously lower strength. Based on the deep excavation project for comprehensive traffic hub of Hengqin Port, the deformation characteristics of foundation pit under thick mud stratum in this area are discussed by using the finite element method. The influences of soil improvement area, embedded depth and stiffness of retaining piles on the deformation of deep foundation pit are analyzed. The deformation control measures and effects of the deep foundation pit for comprehensive traffic hub of Hengqin Port are summarized. It is expected to provide guidance for the design and construction of deep foundation pits in thick mud stratum in this area.