During CO2 storage in deep saline aquifers, the presence of residual water has an important influence on the storage efficiency and safety. In this study, natural rock cores taken from deep reservoirs in the Ordos Basin and Fukang, Xinjiang are used as research objects. Nine groups of core‐flooding experiments are performed under different CO2/N2 gas mixture ratios to study the influence of rock properties (mineral composition, permeability, porosity and pore structure) on the residual water. Furthermore, the geophysical and chemical properties of rock cores are analyzed by X‐ray diffraction, electron microscopy, field emission scanning electron microscopy and piezoelectric mercury method. The results show that residual water saturation is a quantitative power function of drainage time. The residual water saturation is positively correlated with the total amount of quartz and feldspar and increases with increasing permeability. Moreover, both the average and median pore throat radius show a strong inverse correlation with irreducible residual water saturation; as these radius increase, the residual water saturation decreases. In contrast, the porosity and maximum pore throat radius display a weaker correlation with irreducible residual water saturation. This study is of great value for engineering practices such as the site selection of CO2 storage projects in saline aquifer and improvement of CO2 storage efficiency. © 2024 Society of Chemical Industry and John Wiley & Sons, Ltd.