Based on the risk categories and self-control capabilities of risks in water source areas, a comprehensive and quantitative risk assessment index system was established using the Zhengrunzhou water source area in Zhenjiang City as an example, and an evaluation method is put forward. The calculation method of the eigenvalue of each index and the risk level grading standards are presented. In calculating eigenvalues, a cumulative risk index was used to represent the impact of the amount and agglomeration intensity of risk sources on the risks of the water source area, and the cumulative risk index was determined using the spatial autocorrelation analysis method. The results show that the risk level of the Zhengrunzhou water source area is at a the medium grade, the main threats influencing the security of this area are the docks located on the shoreline within 20 km upstream of this area, and the directly discharged pollutants from enterprises and sewage plants have less influence on the water source area.