It is very important to study the evolutionary process of structural of rivercrossing shield tunnel in silt stratum and the structural safety evaluation method. Hence, by using beam element embedded mode, a 3D numerical simulation and calculation model for shield structure of land and water connection section of Sutong GIL Utility Tunnel in silt stratum is established considering oblique bolt connection structure; the stress distribution law and development process of deformation damage of segment structure under the actions of deposition and beaching are analyzed; the evolutionary process of structural mechanical damage under the action of external force is revealed; and the deformation control standards and the safety evaluation standards based on the most unfavorable condition of the tunnel structure in silt stratum are proposed by case study. The study results show that: (1) The sequence of structural damage under the actions of deposition and beaching is the uniaxial compressive strength of concrete, triaxial compressive strength of concrete and the yield of steel; and the tunnel vertical convergences are 60.6 mm, 81 mm and 113.8 mm and 86.1 mm, 117.2 mm and 147.9 mm under the actions of deposition and beaching, respectively. (2) The tunnel vertical convergence induced by the action of beaching is 1.3-1.5 times that induced by the action of deposition; and the calculated results coincide with the actual data. (3) The easilycollected deformation monitoring indices, i.e. rebar stress, bolt axial force and joint open, should be selected; and a 4level safety evaluation standard should be determined according to the structural mechanical damage and the requirements of design.