Technology of hydrate-based CO2 separation and capture is considered as a green and economical gas separation technology and is extensively studied. Most of the previous studies involving the aspects of thermodynamics and kinetics of the CO2 gas hydrate formation were carried out with small reactors, whereas few studies were carried out with pilot-scale equipments. In this paper, a pilot-scale CO2 separation from flue gas by the hydrate method is reported. By the equipment, we successfully realize CO2 separation from flue gas. By a two-stage hydrate separation process, the CO2 concentration can be enhanced to approximately 90.0% from 17.0%. The effects of the operating pressure and gas flow rate on CO2 recovery are also investigated by comparing and analyzing the data of the CO2 concentration, gas consumption, and CO2 recovery. The higher pressure results in the higher CO2 recovery, and there is an optimal ratio of the gas flow rate to the fluid flow rate for obtaining the highest gas consumption. The results achieved in this paper will be an important foundation to further develop the continuous CO2 hydrate separation process.