Shale oil in China is widely distributed and has enormous resource potential. The pores of shale are at the nanoscale, and traditional research methods encounter difficulty in accurately describing the fluid flow mechanism, which has become a bottleneck restricting the industrial development of shale oil in China. To clarify the distribution and migration laws of fluid microstructure in shale nanopores, we constructed a heterogeneous inorganic composite shale model and explored the fluid behavior in different regions of heterogeneous surfaces. The results revealed the adsorption capacity for alkanes in the quartz region was stronger than that in the illite region. When the aperture was small, solid–liquid interactions dominated; as the aperture increased, the bulk fluid achieved a more uniform and higher flow rate. Under conditions of small aperture/low temperature/low pressure gradient, the quartz region maintained a negative slip boundary. Illite was more hydrophilic than quartz; when the water content was low, water molecules formed a “liquid film” on the illite surface, and the oil flux percentages in the illite and quartz regions were 87% and 99%, respectively. At 50% water content, the adsorbed water in the illite region reached saturation, the quartz region remained unsaturated, and the difference in the oil flux percentage of the two regions decreased. At 70% water content, the adsorbed water in the two regions reached a fully saturated state, and a layered structure of “water–two-phase region–water” was formed in the heterogeneous nanopore. This study is of great significance for understanding the occurrence characteristics and flow mechanism of shale oil within inorganic nanopores.