Abstract In this chapter, we review knowledge critical to simulating hydrate formation and dissociation in marine sediments. The advantages and disadvantages of existing numerical models are summarized. An advanced computational model (meshless-particle-based model) is introduced to simulate fluid flow, heat and mass transfer, and hydrate formation at the pore level. In the model, the spatial distribution and uncertainty of porosity and variation of permeability with hydrate formation can be predicted. The model has been tested for different crystal growth kinetics. The pore-level simulation results may help us understand the quantity and distribution of methane hydrate within the confines of a pore space.