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Hydrate distribution heterogeneity is often observed in natural and artificial hydrate-bearing sediments (HBSs). To capture hydrate distribution heterogeneity, a pore-scale method is proposed to model cemented HBSs using the discrete element method (DEM). This method takes into account the quantitative effect of hydrate saturation in a sediment pore on the contact bond parameters surrounding the pore. A series of DEM specimens with different macroscopically and microscopically heterogeneous hydrate distributions are prepared. The mechanical behavior of heterogeneous HBSs is investigated by performing biaxial compression tests with flexible boundaries. The simulation results show that both macroscopic and microscopic hydrate distribution heterogeneity can influence the mechanical properties of HBSs. The shear strength is promoted in both macroscopically and microscopically heterogeneous HBSs. Longitudinally heterogeneous HBSs have a higher secant modulus, while transversely heterogeneous HBSs have a lower secant modulus than homogeneous HBSs. The secant modulus of microscopically heterogeneous HBSs first increases and then decreases with increasing pore hydrate saturation. It is found that the deformation behavior and bond breakage evolution of HBSs depend on hydrate distribution heterogeneity. These findings can provide insights into understanding the mechanical behavior of natural HBSs with heterogeneous hydrate distributions.