As one of the major engineering disasters in tunnel structures, segment lining cracks have significant impacts on the carrying capacity and durability of shield tunnels. This study focused on the lining cracking problems that are induced by annular interfacial unevenness during construction; a three-dimensional finite element model of shield tunnel linings was established that uses particular gasket elements and considers the assembly tolerance between segments and dowel pads at the annular interface. Through the numerical simulation, the lining’s structural deformation and crack propagation in the presence of the annular joint’s unevenness were studied by adjusting the initial gap and the normal stiffness modulus of the dowel pad at the annular interface. The numerical results indicate that the cracks induced by the jacking thrust force are initiated in hang holes in the midspan of the segments and subsequently develop along the longitudinal direction. In addition, the critical thrust loads for crack occurrence and the crack length are directly related to the initial gap and the stiffness modulus of the dowel pads at the annular interface of the segments. Moreover, the higher the assembly tolerance and the dowel pad stiffness modulus, the more serious will be the longitudinal cracks. It is confirmed that the use of appropriate dowel pads can effectively control the initiation and development of longitudinal cracks and enhance the structure’s carrying capacity.