A multi-phase extraction technology was implemented to reduce the source of pollutants within a large retired chemical area in Shanghai, prevent further diffusion, and lower the health and ecological risks associated with the pollutants, while simultaneously analyzing the characteristics of NAPLs under the influence of multi-phase extraction. Through monitoring pollutants in the shallow groundwater across the site, changes in the spatial distribution of pollutants in the aquifer under extraction influence were characterized and ecological risks were assessed. The study indicated that the one-year multi-phase extraction project was significantly effective, with removal rates of pollutants in heavily contaminated areas reaching 64.56% to 99.26% at varying depths. A high degree of homogeneity and spatial autocorrelation was maintained among NAPLs prior to extraction, with correlation coefficients ranging from 0.26 to 0.72. The extraction process influenced the distribution and concentration of pollutants, resulting in changes in the correlations among them. The content and depth of DNAPLs in the site maintained a significant positive correlation, while LNAPLs exhibited a negative correlation. Under the extraction influence, the spatial distribution fitting of pollutants showed a substantial reduction in the central area and surrounding contamination halo, with the range of 1,4-dichlorobenzene pollution experiencing the largest decline, reducing the contaminated area by 91.98%. The assessment indicated that the proportion of high ecological risk points within the site significantly decreased post-extraction, and the multi-phase extraction comprehensively reduced the ecological risk of the site. However, some points of medium to high ecological risk still exist (primarily related to total petroleum hydrocarbon pollutants), which should be monitored and addressed in future remediation efforts.