In-situ pyrolysis of oil shale is an economical and environmental friendly technology. During the process of in-situ pyrolysis of oil shale, the changes of temperature cause the decomposition of kerogen and the conversion of clay minerals in oil shale, which vary the porosity and permeability of oil shale, and the porosity and permeability of oil shale are important factors for migration of the hydrocarbons. In order to study the changes of porosity and permeability during the in-situ pyrolysis of oil shale, A three-dimensional model referring to the field tests of in-situ pyrolysis of oil shale in Songyuan City, Jilin Province and modified to hexagonal well pattern was established, and the numerical simulations of the processes of heating, hydrocarbon generation, clay mineral conversion, and changes in porosity and permeability during the in-situ pyrolysis of oil shale were conducted. The results show that the porosity and permeability of oil shale show an increasing trend with the hydrocarbon generation process during the in-situ pyrolysis of oil shale, and the growth rate is faster then slower. When the hot gas is injected for 1000 days, the porosity increases by 3.37% and the permeability increased by 0.0049 (10-3μm2). The porosity of oil shale increases with the conversion of montmorillonite to illite, and the conversion of montmorillonite to illite increases the permeability. When the hot gas is injected for 1000 days, the porosity increased by 2.14% and the permeability increased by 0.0025 (10-3μm2).