Due to the increase in environmental concerns and the environmental regulations enacted by governments, green supply chain has received more attention. In this paper, a mixed-integer linear programming model is presented for supply chain planning under emission trading scheme in which carbon footprints is considered in transportation, storage and production. Moreover, since machine upgrade would influence carbon emission, the model has been powered with the ability to decide in which planning periods these upgrades should take place. The model is validated by examining a hypothetical example.