Optimizing highway design can help reduce carbon emissions throughout the entire life cycle of highways. To analyze the carbon reduction benefits of highway design optimization, the carbon emission factor method was used to develop a model for calculating the carbon reduction benefits of design optimization. Using an expressway in the Guangdong-Hong Kong-Macao Greater Bay Area as a case study, the carbon reduction benefits from various design optimizations—such as shortening the route length, sharing traffic corridors with local roads, and optimizing interchange type—were calculated. The study results show that design optimization during the planning stage has a significant impact on carbon reduction. The case project achieved a total reduction of 1.88 × 108 kg of carbon emissions. The carbon reduction benefits of the three design optimizations, ranked from greatest to least, were: shortening the route length (1.43 × 108 kg) > optimizing the interchange design (4.47 × 107 kg) > sharing traffic corridors with local roads (5.92 × 105 kg). Material savings contributed the most to carbon reduction, with route shortening and interchanges type optimization accounting for 93.90% and 92.13% of the total carbon reductions, respectively, mainly due to the reduced use of steel bar and cement. The carbon reduction benefits from energy savings were greater than those from land-use savings, and the contribution of electricity savings exceeded that of fossil fuels such as diesel, gasoline, and fuel oil. Accordingly, efforts to reduce carbon emissions at the design stage of highways should be strengthened by evaluating design alternatives in terms of project scale, construction schemes, low-carbon materials, and construction conditions, thereby promoting the development of low-carbon highway infrastructure.