The uncertainty issue becoming more and more important in term of freight transport, which essentially affect the transport cost. As an essential parameter to construct the product price, the transport cost variations sequentially impact the supply chain network structures. This paper then presents the multi-channelled supply chain network equilibrium (SCNE) model with the behaviour of freight carriers by considering variation of travel time. The cocoa SCNE model is then invoked to represent the trading chain of cocoa. As different with the previous researches, the model takes into account the variation of traffic flow and the road capacity to the freight cycle time, which is practically used for estimating the transport cost. The variation is propagated based on the Monte Carlo simulation approach. Finally, the model is applied to an actual cocoa SCN in Sulawesi for investigating the impact of travel time variation to the price of cocoa.