Intermodal freight transport is the movement of goods in one and the same loading unit or vehicle by successive modes of transport without handling of the goods themselves when hanging modes. During the whole intermodal operation process, the multi-side participation is an outstanding feature, and how to Coordination behaviors among the multi-actor's is a core problem, which has been considered a challenging issue by many practitioners and researchers. However, it is still in a pre-paradigmatic phase as a new transportation research application field.In this paper, coordination mechanisms are studied through penalty schemes among different carriers which cooperation together to make transport capacity distribute plan in the rail-road intermodal freight transport market. It's assumend that, in a duopoly freight transport market, there are two separate transport firms with complementary transport model cooperation to develop a long haul intermodal freight service. Firm I is the first segment carrier for offering ground transport service and firm II is the second segment carrier for offering rail transport service. Two possible organizational structures, i.e. centralized and decentralized are taken into consideration. In the centralized case—the first best case as a benchmark, wherein two firms jointly decide on the transport capacity distribute plan. In the decentralized case, a Stackelberg game model is formulated. Firm I is the Stackelberg leader with the constraint service level and firm II is the follower. Two firm's behavior strategic is first analyzed without considering the coordination by the penalty scheme in the decentralized system. After considering the different cost structure and opportunistic behaviors for two separate carriers, the solution equilibrium shows it is never optimal for firm II to make more than the demand estimate specified by firm I, therefore, carrier I has overestimate incentive and carrier II has undersupply incentive on transport capacity distribute decision making. In order to coordinate the decisions, the suitable penalty scheme is designed to coordinate two firm's behavior necessarily. Second, based on the decisions which is made in thecentralized system—the first best case and as a benchmark, the coordination is analyzed by setting suitable penalties. This study shows that by setting the suitable penalties one can generate the same result in a decentralized system as that obtained from a centralized system. It is also discussed in details the effective range of penalties to coordinate two firm's decision. The further study shows, It's not necessary to setting higher penalty to the overestimate behavior of carrier I, the penalty for overestimate is in a specific interval which is influenced by parameter K(in effect, that is a bargain power to customer), otherwise, the final transport capacity would be reduced by setting the too higher penalty. The lower bound of penalty for undersupply to carrier II, meanwhile, is also proved. The penalties would facilitate to increase the final intermodal transport capacity. In the end, a numerical example is provided to verify the validity of conclusions, and then some concluding remarks are presented finally.