In the present study, a 3-dimensional (3D) numerical model was developed to mimic the micro porous structure of a geological $CO_2$ storage reservoir. Especially, 3D modeling technique assigning random pore size to a 3D micro porous structure was devised. Numerical method using CFD (computational fluid dynamics) was applied for the 3D micro porous structure to calculate supercritical $CO_2$ flow field. The three different configurations of 3D micro porous model were designed and their flow fields were calculated. For the physical conditions of $CO_2$ flow, temperature and pressure were set up equivalent to geological underground condition where $CO_2$ fluid was stored. From the results, the characteristics of the supercritical $CO_2$ flow fields were scrutinized and the influence of the micro pore configuration on the flow field was investigated. In particular, the pressure difference and consequent $CO_2$ permeability were calculated and compared with increasing $CO_2$ flow rate.