Urbanization is considered a main indicator of regional economic development due to its positive effect on promoting industrial development; however, many regions, especially developing countries, have troubled in its negative effect—the aggravating environmental pollution. Many researchers have addressed that the rapid urbanization stimulated the expansion of the industrial production and increased the industrial pollutant emissions. However, this statement is exposed to a grave drawback in that urbanization not only expands industrial production but also improves labor productivity and changes industrial structure. To make up this drawback, we first decompose the influence of urbanization impacts on the industrial pollutant emissions into the scale effect, the intensive effect, and the structure effect by using the Kaya Identity and the LMDI Method; second, we perform an empirical study of the three effects by applying the spatial panel model on the basis of the data from 282 prefecture-level cities of China from 2003 to 2014. Our results indicate that (1) there are significant reverse U-shapes between China’s urbanization rate and the volume of industrial wastewater discharge, sulfur dioxide emissions and soot (dust) emissions; (2) the relationship between China’s urbanization and the industrial pollutant emissions depends on the scale effect, the intensive effect and the structure effect jointly. Specifically, the scale effect and the structure effect tend to aggravate the industrial wastewater discharge, the sulfur dioxide emissions and the soot (dust) emissions in China’s cities, while the intensive effect results in decreasing the three types of industrial pollutant emissions; (3) there are significant spatial autocorrelations of the industrial pollutant emissions among China’s cities, but the spatial spillover effect is non-existent or non-significant. We attempt to explain this contradiction due to the fact that the vast rural areas around China’s cities serve as sponge belts and absorb the spatial spillover of the industrial pollutant emissions from cities. According to the results, we argue the decomposition of the three effects is necessary and meaningful, it establishes a cornerstone in understanding the definite relationship between urbanization and industrial pollutant emissions, and effectively contributes to the relative policy making.