Trifluoromethane (CHF3) is a ubiquitous by-product of chlorodifluoromethane synthesis (CHCIF2) and is regarded as one of the most potent greenhouse emissions. Despite the adverse effects on the environment, CHF3 is the general method of exhaust gas incineration and is used for other purposes, for example, as a coolant and in plasma etching. This project establishes a flexible and efficient two-stage vacuum pressure swing adsorption (VPSA) process to generate pure CHF3 and CHCIF2 simultaneously, improving the product's recovery rate. The first-stage VPSA unit loading activated carbon is developed to obtain CHF3 with the purity of 99%. CHCIF2 of 99.5% purity is obtained from the second-stage VPSA unit with NaX zeolite. The process simulation predicts that the two-stage coupled VPSA separation system can obtain CHF3 and CHCIF2 simultaneously. Under the best process parameters, the purity of CHF3, the recovery rate of CHF3, the purity of CHCIF2, and the recovery rate of CHCIF2 are 99, 77.71, 99.5, and 72.13%, respectively. In all, our research demonstrates that the two-stage VPSA system is a practicable and worthy prospect for research and development. In addition, it can recover and purify CHF3 and CHCIF2 through an efficient and cost-effective method.