Animal manure used to be the major source of additional nutrients and crucial for maintaining soil fertility and crop yield in traditional farming systems. However, it is increasingly not recycled, wasting vital resources and damaging the environment. By using long-term (1986–2017) data from a rural household survey (>20,000 households) across China, here we show that the share of rural households with both crop planting and livestock raising (CPLR) has sharply declined from 71% in 1986 to only 12% in 2017. Compared with households with only crop planting, the CPLR households apply less synthetic fertilizer and more manure per cropland area. However, manure production in one-third of CPLR households has exceeded the nutrient requirement of crop growth on their croplands. Rebuilding the links between livestock and croplands at a regional scale thus provides vital opportunities for the sustainable intensification of agriculture in China.