As an effective measure to promote socio-economic development, industrial transformation indirectly changes the characteristics of urban underlying surfaces, leading to the complexity of controlling nonpoint source (NPS) pollution in cities. However, the relationship between industrial transformation and urban NPS pollution, as well as the critical socioeconomic factors influencing the characteristics of urban NPS pollution during the period of industrial transformation, is still unclear, seriously affecting urban water environment management. In this research, indicator systems for the estimation of industrial transformation and urban NPS pollution were first established. Then, the characteristics of industrial transformation and urban NPS pollution were analyzed through an entropy weight method and a volume–concentration model. In addition, critical socioeconomic factors affecting urban NPS pollution during periods of industrial transformation were identified using Pearson correlation analysis and a grey correlation model. Using Dongguan City in South China as the study area, the results showed that the level of industrial transformation in this city shows an upward trend, and the towns with relatively high level of industrial transformation gradually gathered around Songshan Lake. The four urban NPS pollution index (i.e., chemical oxygen demand, suspended solids, total nitrogen, and total phosphorus) significantly increased during the slow transformation period (2000–2010), then slightly decreased during the rapid transformation period (2010–2020). The pollution loads exhibited significant spatiotemporal heterogeneity. A significantly negative correlation (p < 0.05) was observed between industrial transformation and urban NPS pollution levels during the transformation period. It was found that fertilizer, electricity, and water consumptions, as well as permanent population were the critical socioeconomic factors affecting urban NPS pollution. Control of the application amounts of fertilizers and improvement in the efficiencies of urban water and electricity use are the effective methods for preventing and controlling urban NPS pollution during the period of industrial transformation. In addition, industrial enterprises should increase their investment in research and development activities to accelerate industrial transformation and reduce the urban NPS pollution load. This research contributes to urban NPS pollution control in the area undergoing industrial transformation.