This study examines the relationship between parasitic infections and agricultural innovations in China during the Song dynasty (960–1279 CE), particularly how the widespread use of night soil (human excrement) as fertilizer affected public health. The introduction of Champa rice and the expansion of double cropping systems substantially increased agricultural productivity and supported population growth but also intensified human–environment interactions that facilitated parasite transmission. The night soil was routinely transported from urban to rural areas to improve soil fertility and crop production, but its untreated application facilitated the local and regional spread of intestinal parasites. Analysis of Song dynasty historical records, including 太平圣惠方 (Peaceful Holy Benevolent Prescriptions), 证类本草 (Classified Herbal Medicine), 陈尃农书 (Chen Fu’s Agricultural Book), reveals a well-developed body of pharmacological knowledge regarding parasitic infections, suggesting that they were a significant health concern. Together with archaeoparasitological findings, this study identifies intestinal parasites – including Ascaris lumbricoides, Trichuris trichiura, Clonorchis sinensis, Enterobius vermicularis and Taenia spp. – as likely to be prevalent during the Song dynasty. Moreover, variations in food consumption, agricultural practices and sanitation systems contributed to distinct regional patterns of parasitic infections. By integrating archaeological data with historical sources, this study demonstrates how agricultural intensification and urban development during the Song dynasty created environmental conditions conducive to pathogen survival, advancing our understanding of the health costs brought by agricultural expansion in ancient China.