Rapid urbanization results in the conversion of natural soil to urban soil, and consequently, the storage and density of the soil carbon pools change. Taking Chongqing Municipality of China as a study case, this investigation attempts to better understand soil carbon pools in hilly cities. First, the vegetated areas in the study area were derived from QuickBird images. Then, topsoil data from 220 soil samples (0–20 cm) in the vegetated areas were collected and their soil organic carbon (SOC) densities were analyzed. Using the Kriging interpolation method, the spatial pattern of SOC was estimated. The results show that the SOC density exhibited high spatial variability in the urban topsoil of Chongqing. First, the SOC density in topsoil decreased according to slope in the order 2°–6° < 25°–90° < 0°–2° < 6°–15° < 15°–25°. Second, the newly developed areas during 2001–2010 had a lower SOC density than the areas built before 1988. Third, urban parks and gardens had a higher SOC density in topsoil, residential green land followed, and scattered street green land ranked last. For hilly cities, the variability of terrain affects the distribution of SOC. The Kriging results indicate that Kriging method combining slope with SOC density produced a high level of accuracy. The Kriging results show that the SOC density to the north of the Jialing River was higher than the south. The vegetated areas were estimated to amount to 73.5 km² across the study area with an SOC storage of 0.192 Tg and an average density of 2.61 kg/m².