Abstract: Global warming has caused widespread concern in the international community，and reducing carbon emissions have reached a consensus. Exploring costs of port cluster transportation network and factors about carbon emission, an optimization model of hybrid Hub-and-Spoke for port cluster transportation network is constructed for the realization of the minimum total cost of port cluster transportation network. Then a numerical example is given to demonstrate the application of the proposed model, and effects of various parameters on the port cluster transportation network are analyzed in-depth. Finally some conclusions are obtained that: the speed of the minimum economic costs is higher than that of the minimize carbon emission cost; sailing speed should be controlled between 18 and 22 knots, and vehicle speed should be controlled within 50 and 60 km/h; most ports chose larger vessels or vehicles directly or through single hub port to destination; carbon emissions weighting, vehicle cost coefficient, and time utility coefficient have greater impact on port cluster transport network. More emphasis on energy conservation, improvement of transport efficiency, attention to the type of goods and time utility, and rational allocation of resources to optimize the network, are effective ways for port cluster to implement energy saving and emission reduction.