Evaluating vehicles’ energy consumption and emissions is significant to ease energy shortages and prevent environmental pollution. This study focuses on evaluating energy consumption and emissions of the mixed traffic flow with human-driven and autonomous vehicles from both economic and environmental perspectives. The proposed Green Cost Model is comprised of the energy consumption models and emissions models, taking energy recovery of electric vehicles and specific power of fuel vehicles into consideration. Based on the Energy, Economic and Environment theory, the fuel price, electricity price and carbon taxation are utilized to analyze the cost of energy usage and emissions. The feasibility and effectiveness of the Green Cost Model are verified by simulations in several typical traffic scenarios. The simulation results indicate the green cost of both fuel powered and electric vehicles. In different scenarios, the electric vehicles have less green cost than fuel vehicles, and the total green cost of the fleet decreases as the penetration of autonomous battery electric vehicles (ABEV) increases. In addition, lower average green cost and higher service level are obtained by taking green cost into account in the intersection timing scheme. Finally, scientific and rational policy implications are put forward for the government, drivers and automakers.