Nearly one quarter of global meat production occurs in China, but a lack of detailed spatial livestock production data hinders ongoing pollution mitigation strategies. Here we generate high-resolution maps of livestock systems in China using over 480,000 farm surveys from 2007 to 2017, finding that China produced more livestock protein with fewer animals and less total pollution impact through better breeding, feeding and manure management in large-scale livestock farms. Hotspots of production can be observed across the North China Plain, Northeastern China and the Sichuan Basin. The Clean Water Act reduced manure nutrient losses to water by one third, but with limited changes to methane and ammonia emissions. Integrated production and consumption abatement measures costing approximately US$6 billion could further reduce livestock pollution by 2050, realizing benefits of up to US$30 billion due to avoided human health and ecosystem costs. © The Author(s), under exclusive licence to Springer Nature Limited 2022.