Nowadays, one of the important issues, is taking greening concerns into account, in supply chain networks related activities. Transportation activities have great part of activities in such networks especially in the case of Biomass supply chains. In this research, we introduce the biomass supply chain structure to show the role of transportation in such network. We concider a network which contains of several zones, some of them have surplus amount of Biomass resources which can be transported to the zones with deficit of resources. We proposed an MIP model, which considers multi transportation modes for transferring Biomass among the zones which are: local road, highway and railroad. Each mode of transportation, leads to specific Carbon Emission Factor and, the amount of Fuel Consumption for transportation vehicle. The objective function intends to minimize the cost of transportation, backorders and warehousing costs, while considering the amount of emitted Carbon FootPrint (CFP) as a result of huge amount of transportation. We solved our proposed model, using LINGO software. The computational results of applying such model to Biomass supply chain network have been presented.