This study examined the relationship between urban compactness and greenhouse gas (GHG) emissions in the road transport sector in South Korea, focusing on 84 cities, particularly 27 metropolitan areas with populations of approximately 500,000. We developed an urban compactness index (UCI) using Moran’s I, entropy, and the Gini coefficient, integrating city size into the analysis. Cities were categorized into five groups based on their size to analyze GHG emissions and regional variations in compactness comparatively. Our results revealed a significant inverse relationship between UCI and per capita road transport GHG emissions, which was more pronounced in larger cities. Specifically, cities with a population over 1 million displayed reduced per capita road transport GHG emissions in compact urban structures. In conclusion, these findings suggest that larger cities can effectively reduce per capita road transport GHG emissions through urban planning for compact development. Additionally, planners need to consider city size when analyzing the UCI and formulating urban planning strategies aimed at achieving carbon neutrality.