Taking the supercritical CO2 (SC‐CO2) Joule–Thomson coefficient and the effects of adsorption between CO2‐shale‐CH4 into consideration, a two‐phase filtration rate calculation model of SC‐CO2 fracturing in unconventional natural gas reservoirs is proposed. With the help of an experimental apparatus of fluid filtration in shales, it has been found that the theoretical calculation and experimental measurement have an absolute error of 3.31% of the steady filtration rate under specific conditions. Under different pressure differentials between the reservoir and the fracture, the absolute average error of the calculated filtration rate is 2.53%, compared with the experimental data. The filtration of the SC‐CO2 fracturing in an unconventional natural gas reservoir is characterized by the filtration rate, which gradually decreases with time, and the rate of its decrease tends to reach equilibrium in the late stage. The funnel‐like pressure distribution occurs near the fracture during the transmission of the filtration pressure. A non‐linear relationship exists between the filtration rate and the permeability, which indicates that higher permeability enlarges the effective range of the fracturing fluid pressure as well as the invasion region. Moreover, the steady filtration rate and the pressure drop magnitude present a nearly linear increase with the increasing filtration pressure differential. In the site operation of the SC‐CO2 fracturing, the injection temperature, pressure, and pump rate can be optimized using the proposed chart. Thickening of the SC‐CO2 fracturing fluid can effectively decrease the filtration rate, and thus development of thickened SC‐CO2 fracturing fluid systems that prevent formation damage is needed. © 2017 Society of Chemical Industry and John Wiley & Sons, Ltd.