In order to analyze the impacts of different carbon allowance allocation rules of the government on independent remanufacturing, a game model between an original equipment manufacturer and an independent remanufacturer was established based on the grandfathering rule and the benchmarking rule. The impacts of the two different carbon allowance allocation rules on the optimal production decisions, profits, and the environment of the members of the closed-loop supply chain were compared. The results show that the lower sales of new products and the higher sales of remanufactured products under the grandfathering rule are more friendly to environmental protection while promoting the development of the remanufacturing industry. The original equipment manufacturer and the independent remanufacturer can realize a win-win profit in the grandfathering rule when the total carbon quota and baseline carbon quota meet specific requirements.