Supersonic separation utilizes the cryogenics created by gas expansion to purify the mixture. This method is a novel carbon capture scheme. In this work, the models of N2-CO2 (flue gas) and CH4-CO2 (natural gas) are established to calculate the condensation flow. The condensation behavior of CO2 in natural gas and flue gas is clarified respectively, and the difference between the two is compared for the first time. Under the same conditions, CO2 in flue gas reaches the limit non-equilibrium state first, forming non-equilibrium condensation with limit nucleation rate of 7.78 × 1020 m−3s−1 and maximum droplet growth rate of 8.19 × 10−3 m s−1. However, the maximum droplet growth rate in natural gas is only 2.22 × 10−3 m s−1, which implies that the interphase mass transfer rate in flue gas is larger during the CO2 condensation. In addition, the condensation behavior of CO2 in natural gas is more sensitive to the changes of inlet parameters. This work provides an invaluable contribution to the development of supersonic carbon capture.