Utility consumptions in hydrotreating (HDT) units are rapidly increasing because more heavy and sour crude oil are being processed to satisfy the increasing market demand of clean fuels, which then cause the direct and indirect emissions of CO2 and SO2. The environmental impacts of utilities should be considered when optimizing an HDT unit. A multi-objective optimization is proposed to reduce the operating cost and environmental impacts of utilities and products based on hydrogenation reaction kinetics. A cracked diesel HDT unit is adopted to illustrate the proposed model which is solved by e-constrains method to obtain the Pareto fronts and three scenarios: minimum operating cost, minimum environmental impacts, and the best compromise. For all scenarios, increasing temperature and decreasing pressure can reduce both the operating cost and environmental impacts. The decreasing of sulfur content in product is at the expense of consuming more utilities. It is not always favorable when the sulfur content of the product is decreasing. Thus, there is an optimum desulfurization degree in the HDT unit when reducing the environmental impacts. Therefore, the environmental impacts of an HDT process, especially for the impacts of the production process, should not be ignored when optimizing an HDT process. The most efficient way to reduce both the operating cost and environmental impacts is to reduce the hydrogen consumption.