Exploring the industrial pollution agglomeration effect of regional integration addresses the collaborative implementation of regional coordinated development and ecological civilization construction strategies. By matching the pollution data of Chinese enterprises from 1998 to 2012 to the city level, this paper uses the regression discontinuity method and the difference-in-differences model to investigate the overall effect of regional integration on industrial pollution agglomeration, as well as the differences between incumbent and entrant cities, from the perspectives of the boundary and enlargement effects in China’s Yangtze River Delta (YRD) region. In particular, two mechanisms of the pollution agglomeration effect: economic agglomeration and industrial division are examined. The results show a clear discontinuity in industrial pollution agglomeration (i.e., a positive industrial pollution agglomeration boundary effect) at the boundary of the YRD region. Fortunately, the enlargement of the YRD region significantly inhibits industrial pollution agglomeration, and such an inhibiting effect varies with different types of cities. In detail, the inhibiting effect on the agglomeration of chemical oxygen demand and sulfur dioxide is significantly stronger in incumbent cities than in entrant cities. The mechanism analysis reveals that economic agglomeration promotes industrial pollution agglomeration, whereas the expansion of the YRD region curbs it by reducing economic agglomeration. Meanwhile, although industrial diversification in the YRD region increases industrial pollution agglomeration, the enlargement reduces industrial pollution agglomeration by inhibiting industrial specialization.