To comply with the regulations of emission control areas (ECAs), most operators have to switch to low-sulfur fuels inside the ECAs. Besides, a low-carbon objective is essential for long-term environmental protection; thus, is regarded as important as making profit. Therefore, the operators start making speed and route decisions under the two objectives of minimizing carbon emissions and maximizing profit. Drawing on existing methods, this paper formulates the profit and carbon emissions in sustainable coastal shipping, investigates the speed and route principles, and determines the best tradeoff between profit and carbon emissions. It is found that vessel speed should be set between emissions-optimum speed and profit-optimum speed, and the route must be selected in light of the speed decision. Next, the optimal choices of speed and route were examined under different scenarios and vessel types. The results show that the operation measures and objectives depend greatly on fuel price, vessel load, and vessel parameters. The operator should speed up the vessel if he/she wants to make more profit or if the scenario is favorable for profit making; e.g., low fuel price and high vessel load (LFHL). Large vessels should pursue more profit under LFHL conditions, without having to sail further outside the ECA. But this rule does not apply to small vessels. In addition, the operator should slow down the vessel inside the ECA and sail further, outside the ECA, with the growth in the price spread between marine gas oil (MGO) and heavy fuel oil (HFO), especially at a low HFO price. The research findings help operators to design operational measures that best suit the limit on sulfur content in fuel and the situation of the shipping market.