Natural hydrate-bearing sediments attract broad attention due to their important role in natural gas extraction and climate change. Their mechanical behavior, governed by hydrate saturation and spatial distribution (i.e. pore habits), requires in-depth understanding. The discrete element method (DEM) serves as an important tool to reveal the micromechanics of particle-hydrate interactions and the macroscopic behavior of hydrate-bearing sediments. However, a comprehensively validated DEM modeling of hydrate-bearing sediments is missing in previous studies. This study introduces a generic DEM-based modeling framework for hydrate-bearing sands, integrating modeling and parameter calibrations for various pore habits. The framework's efficacy is demonstrated through calibration against triaxial tests of hydrate, sand, and hydrate-bearing sands, yielding close agreement between the experimental observations and simulation results. Utilizing this modeling framework, the impact of pore habits on the mechanical behavior of hydrate-bearing sands is investigated. Results show that the strength and stiffness of hydrate-bearing sands are significantly enhanced by the presence of hydrate, and this enhancement is modulated by hydrate pore habits. In addition, compared with pure sand, hydrate-bearing sand exhibits a narrower shear band, a lower particle rotation angle, and a more brittle failure pattern. The findings advocate for considering hydrate pore habits to accurately predict sediment behavior.