Oil transport is greatly affected by heterogeneous pore–throat structures present in shale. It is therefore very important to accurately characterize pore–throat structures. Additionally, it remains unclear how pore–throat structures affect oil transport capacity. In this paper, using finite element (FE) simulation and mathematical modeling, we calculated the hydrodynamic resistance for four pore–throat structure. In addition, the influence of pore throat structure on shale oil permeability is analyzed. According to the results, the hydrodynamic resistance of different pore throat structures can vary by 300%. The contribution of additional resistance caused by streamline bending is also in excess of 40%, even without slip length. Furthermore, Pore–throat structures can affect apparent permeability by more than 60% on the REV scale, and this influence increases with heterogeneity of pore size distribution, organic matter content, and organic matter number. Clearly, modeling shale oil flow requires consideration of porous–throat structure and additional resistance, otherwise oil recovery and flow capacity may be overestimated.