Based on the mechanical experimental results of methane hydrate (MH), a bond contact model considering the rate-dependency of MH is proposed. A CFD–DEM scheme considering fluid compressibility is used to simulate a series of undrained cyclic shear tests of numerical methane-hydrate-bearing sediment (MHBS) samples. The dynamic behavior, including stress–strain relationship, dynamic shear modulus, and damping ratio, is investigated. In addition, the force chains, contact fabric and averaged pure rotation rate (APR) are examined to investigate the relationships between micromechanical variables and macromechanical responses in the DEM MH samples. The effects of temperature, confining pressure and MH saturation are also analyzed. Due to the micro-structural strengthening by the MH bonds, no obvious change in microscopic quantities is observed, and the samples remain at the elastic stage under the applied low-shear stress level. When confining pressure and MH saturation increase, the dynamic elastic modulus increases, while the damping ratio decreases. An increasing temperature (leading to weakening of MH bonds) can lower the dynamic elastic modulus, but has almost no impact on the damping ratio. On the contrary, an increasing cyclic shear stress level lowers the damping ratio, but has almost no effect on the dynamic elastic modulus.