A pore-scale numerical simulation was carried out in this study to predict the natural convection in a cubic cavity filled with reconstructed porous medium using lattice Boltzmann Method (LBM). The computational porous domain was established with the micro-computed tomography technique. The natural convection phenomena were predicted with the pore-scale simulation for different thermal boundary conditions and fluid thermal properties. The results show that the natural convection in the present porous domain is more obvious as the side wall is heated compared to that as the bottom wall is heated. The existence of porous structure suppresses the natural convection in the cubic cavity. As Rayleigh number increases, the natural convection in the porous domain is enhanced accordingly. The heat flux distribution on the porous structure surface varies intensively due to the complex flow characteristic in the small pore spaces. The numerical approach presented in this study is to provide a promising solution that can simulate pore-scale natural convection in porous medium and can be further extended for the development of field-scale model for transport processes in porous medium.