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In this paper, an improved mathematical model is proposed to solve the multi-echelon biomass supply chain synthesis problem, including processing hubs selection, biomass allocation design and transportation mode selection, with the consideration of vehicle capacity constraint (weight and volume). On top of that, carbon emission penalty is introduced in the model in order to evaluate the environmental impact in the supply chain. The entire problem is modelled through mixed integer non-linear programming with the aim of maximising the overall profit, at the same time ensuring the minimal CO 2 emission. A comparative study between the model developed in the previous work (vehicle capacity constraint and environmental performance are not considered) and the current improved model is carried out to compare the reliability of the outcomes. Both models are illustrated by using a same case study in Johor, Malaysia. In order to fill the gap of lacking user-friendly decision-making tool for the transportation design in supply chain management, a novel graphical decision-making tool, called smart vehicle selection diagram is proposed in this paper. The diagrams are constructed based on the optimised results obtained from the formulated model. The user manual for the proposed decision-making tool is given in this paper. Besides, five sets of sensitivity analysis are conducted to identify the sensitivity of the assumed realistic factors (i.e. terrain profile, weather changes, traffic congestion, fuel price fluctuation and individual environmental preference) to the optimal results obtained from the proposed tools. This paper shows the potential of the proposed tools in providing rigid optimal solution for the proposed research problem. Finally, several potential future works is suggested in this paper to fill up some of the remaining research gaps. [ABSTRACT FROM AUTHOR]