We consider a capital constrained timber and carbon sink supply chain under the cap-and-trade scheme, where the forest company produces timber and carbon sink. We consider two subsidy modes: financing subsidy to the carbon sink forests and financing subsidy to the manufacturer’s emission reductions. We apply a Stackelberg model and mainly consider the impact of subsidies on the profits and the strategies of the supply chain members. The results show that when the government gives a financing subsidy to the carbon sink forests, it is conducive to promoting the expansion of carbon sink forests, as well as the enhancement of the forest company’s profit. However, a larger supply of carbon sinks generates a lower price, which leads to the manufacturer reducing the technical emission reduction level and purchasing more carbon emission rights instead. On the other hand, when the manufacturer receives a financing subsidy for the technical emission reduction costs, its production becomes cleaner than before, and the profits of the forest company and the manufacturer increase.