For studying the influence of channel dredging on underwater tunnel structure, taking subsea tunnel in the landsea connecting area for example, the surrounding rock is modeled as continuous media based on DruckerPrager yield criterion. The influencing degrees of the channel dredging, including the channel dredging gradient, the alluvium thickness and the dredging working procedure, etc, on tunnel structure deformation and stress are studied by means of finite element software ANSYS. The numerical calculation results show that: 1) The differential deformations along the longitudinal direction of tunnel is increased by channel dredging; the vertical displacement of tunnel roof at underwater section is the largest; and the equivalent stresses of the both sides of tunnel are the largest. 2) The grading gradient is related to slope; the change of gradient affects structure in land and water a little, and mainly affects the deformation and stress of structure in grading section. 3) The influence of backsilting and desilting thickness on structural deformation and internal force should also be considered in the channel planning and design phases.