Most of the greenhouse gas (GHG) emissions in the United States come from the transportation and electricity generation sectors. In this paper, we analyzed the possibility of cross-sector cooperation to cost-efficiently reduce these emissions. Specifically, we built a bi-level optimization model with renewable energy certificate (REC) purchasing to evaluate the effectiveness of the REC purchasing policy. This policy allows the transportation sector to purchase RECs, which are created by renewable generators built by the electricity generation sector, in order to gain extra emission allowance. We conclude from simulations that REC purchasing policy helps to lower the total cost to society while reducing GHG emissions significantly. Simulation results also show that REC purchasing policy can create electricity capacity beyond demand, which can potentially be used to make clean fuel and further cut emissions from existing fossil fuel powered vehicles.