The low-permeability reservoirs have abundant reserves and broad development prospects, and the supplementary energy methods have gradually become a hot research topic. In addition, the technology of enhanced oil recovery through supercritical CO2 injection is becoming increasingly mature; however, the changes in reservoir properties at the microscopic level still need further investigation. In this study, natural rock cores from low-permeability reservoirs were used to simulate reservoir conditions and conduct supercritical CO2 injection experiments for energy supplementation. The study aimed to investigate the changes in reservoir microstructure, minerals, and crude oil properties before and after the experiments. The research results indicate that after supercritical CO2 injection into the reservoir, it dissolves in the formation water to form carbonic acid. Under the effect of dissolution, the porosity of the low-permeability reservoir increases by 1.06–5.68%, and permeability can be improved by 40–60%. The rock becomes more water-wet and less oil-wet. The content of calcite and feldspar in the rock minerals decreases due to the dissolution of carbonic acid, resulting in a reduction in plagioclase and calcite. After the CO2 injection, the light components (C8–C10) in the crude oil in the rock cores decreased by approximately 14.6%, while the heavy components (C16–C39) increased by 6.99%. The viscosity of the crude oil decreases, and its flowability is further enhanced.