Conventional CFD (Computational Fluid Dynamics)-DEM (Discrete Element Method) coupling methods encounter apparent difficulties in addressing the large deformation exhibited by soils with arbitrarily shaped fluid domains for undrained triaxial shear tests with flexible membranes. Herein, a novel CFD-DEM coupling method is proposed to address the main challenges of dynamically reproducing complex external boundaries and mapping for fluid fields. The workflow of surface mesh construction, mesh coarsening, and internal volume division is proposed to generate required meshes. The mapping of fluid information between updated and original meshes is implemented by a distance-weighted interpolation strategy. The coupling method is subsequently applied to investigate the effect of flexible membranes with and without clamped ends on undrained triaxial shear characteristics of soils after its comparison to the constant volume method for validation. The flexible membranes without clamped ends are proven to delay the shear dilation and weaken the inter-particle contact force. Moreover, they enable the free development of the shear band and induce significant octahedral shear strain at both ends of the band. The fluid pressure distributions of both boundary types are uniform and a vortex-shaped velocity field for the fluid is obtained due to the effect of the particle-fluid interaction.