While establishing ultra-deep vertical shafts, there are construction risks and technical difficulties when employing traditional open-cut or caisson methods in water-rich and weak strata. To mitigate these difficulties, this study examines the design points and key technologies of prefabricated ultra-deep vertical shafts in soft and water-rich strata. A case study is conducted on the vertical-shaft sinking machine construction method based on the Chongtai Yangtze River Tunnel No. 2 vertical-shaft project of the Shanghai-Chongqing-Chengdu High-speed Railway. Because the prefabricated vertical-shaft structure should be secondarily opened in large-diameter shield tunneling, the overall stiffness of the prefabricated vertical-shaft structure was enhanced with a novel type of prefabricated vertical-shaft segment structure system. The entire sinking and drilling construction process is simulated in extremely orthogonal anisotropic and isotropic structures using a three-dimensional finite element model. The stress and deformation characteristics are systematically analyzed before and after secondary drilling of the structure. Main findings are as follows: (1) The novel wing-shaped universal segment effectively enhances the overall stiffness of prefabricated vertical shafts facing secondary openings, thereby avoiding the problems of traditional segment circumferential bolt retightening and bolt hole waterproofing. The combination of prefabricated and cast-in-place structures can be utilized to establish a three-dimensional reinforcement structure system for double-sided perforated prefabricated vertical shafts and a comprehensive waterproof system for general prefabricated vertical shafts. (2) Highly orthogonal anisotropic structures and isotropic structures are structurally weaker in the horizontal and vertical directions, respectively, necessitating envelope calculations during structural design. (3) The secondary opening of large-diameter shield tunneling dramatically affects the structural stress, and the vertical stress of the structure requires special attention. The reinforcement of the corresponding segments should be strengthened.