Although Industry 4.0 has transformed the operating model of manufacturing and international trade, no previous research has explored the influence of intelligent manufacturing (IM) on export diversification from a cross-border e-commerce (CBEC) perspective. We use a unique dataset of China’s leading cross-border logistics enterprises to investigate the effect of IM on CBEC export diversification. Our results reveal a positive effect of IM on CBEC export diversification at both market and product levels. This conclusion remains valid after a series of robustness tests. The heterogeneity analysis shows that IM contributes more strongly to diversification of CBEC exports for differentiated products and consumer goods. The mechanistic analysis suggests that IM enables export diversification by stimulating input, output and commercialization of innovation.