[Objective] A study was conducted to understand the heavy metal pollution characteristics of rainwater runoff on different underlying surfaces and the health risks of heavy metal elements in rainwater runoff for the human body. The goal was to provide reference for runoff pollution control in the construction of a sponge city in a mountainous region and provide basic data for human health protection.[Methods] The rainwater runoff of four typical underlying surfaces for a roof, road, parking lot, and square was sampled and monitored at Chongqing Jiaotong University on July 22, 2019. The even mean concentrations, electric conductivity, sodium adsorption rate, hazard quotient, and hazard index were statistically analyzed.[Results] The overall change of heavy metal elements fluctuates greatly during the square runoff process. The health risk of heavy metals in rainwater runoff on roads was the largest, and that of runoff on roofs was the smallest. The large amount of multiple metal pollutants showed a decrease in 10 min after the runoff. The decreases in Fe and Mn were the largest, the decrease in Zn was moderate, and the decrease in Cu was the lowest. As and Cr were the heavy metal pollutants with the highest health risks in rainwater runoff.[Conclusion] Heavy metal pollutants scour faster in a mountainous campus. The heavy metal elements in rainwater runoff of the underlying surfaces with a large human flow fluctuate greatly, but the health risk is low. Heavy metal elements in rainwater runoff of the underlying surfaces with heavy traffic flow have more-stable fluctuations, but they have higher health risks.