Research on the physicochemical reactions between supercritical carbon dioxide (Sc-CO₂) and shale at different temperature is essential for geological CO₂ sequestration. In this paper, shale from the Longmaxi formation in Sichuan basin of China was collected to study the changes in mineral composition, pore structure, and organic functional groups treated with Sc-CO₂ at fixed pressure 8 MPa and temperatures 40 °C to 80 °C. Samples were analyzed with x-ray diffraction, CO₂/N₂ gas adsorption, and Fourier transform infrared spectroscopy. The results show that the dissolution of clay minerals by Sc-CO₂ first declined, but then increased when the temperature increased; dissolution reached a minimum at 60 °C. The specific surface area, total pore volume, predominant pore type (mesopores), and fractal dimension of the shale pore structure first increases and then decreases with increasing temperature. The destruction of hydroxyl structures by Sc-CO₂ is related to the destruction of OH–N and ring hydroxyls. As the temperature increases, the hydroxyl destruction first increases and then decreases. The aromatic hydrocarbons are mainly dominated by 3H and 2H, and their abundances increase significantly as temperature increases, whereas the 4H shows a decreasing trend; the 1H abundance does not change appreciably. The relative abundances of aromatic and aliphatic hydrocarbons decrease linearly as the temperature increases. These research results provide theoretical support for the geological storage of Sc-CO₂ in shale at different temperatures.