Currently, the technology of $CO_2$ capture and storage (CCS) has become the main issue for climate change and global warming. Among CCS technologies, the prediction of $CO_2$ behavior underground is very critical for $CO_2$ storage design, especially for its safety. Hence, the purpose of this paper is to model and simulate $CO_2$ flow and its heat transfer characteristics in a storage site, for more accurate evaluation of the safety for $CO_2$ storage process. In the present study, as part of the storage design, a micro pore-scale model was developed to mimic real porous structure, and computational fluid dynamics was applied to calculate the $CO_2$ flow and thermal fields in the micro pore-scale porous structure. Three different configurations of 3-dimensional (3D) micro-pore structures were developed, and compared. In particular, the technique of assigning random pore size in 3D porous media was considered. For the computation, physical conditions such as temperature and pressure were set up, equivalent to the underground condition at which the $CO_2$ fluid was injected. From the results, the characteristics of the flow and thermal fields of $CO_2$ were scrutinized, and the influence of the configuration of the micro-pore structure on the flow and scalar transport was investigated.