The emission control technologies decisions of port and shipping enterprises under subsidy and customers’ low-carbon preferences are discussed from a supply chain perspective. The game models are established under three game models (port-leader Stackelberg game, ship-leader Stackelberg game, and Nash game). The obtained results show that the impact of subsidy and low-carbon preference on demand in its pricing always is considered by the leader in the port supply chain. The profits and emissions in the Nash game are higher than that in the Stackelberg game. When subsidies and customers’ low-carbon preferences are low, the supply chain’s overall profits of using low sulfur oil are higher than that of using shore power. But the supply chain’s carbon emissions of adopting low sulfur oil are also higher than that of adopting shore power. When subsidies and low-carbon preferences of customers are high, the supply chain’s overall profits of using shore power are higher than that of using low sulfur oil. But the supply chain’s carbon emissions of adopting shore power are also higher than that of adopting low sulfur oil. When subsidy and low-carbon preference of customers are in the appropriate(medial) range, the supply chain would choose shore power to reduce emissions from the perspective of profits, and the whole carbon emissions of using shore power are lower than that of using low sulfur oil, so the regulator(government) and enterprises can achieve a win-win situation. Hence for a regulator who has to balance emission control and enterprises’ profits, implementing moderate subsidy within the appropriate range is the better strategy.