The largest livestock production and greatest fertilizer use in the world occurs in China. However, quantification of the nutrient flows through the manure management chain and their interactions with management-related measures is lacking. Herein, we present a detailed analysis of the nutrient flows and losses in the “feed intake–excretion–housing–storage–treatment–application” manure chain, while considering differences among livestock production systems. We estimated the environmental loss from the manure chain in 2010 to be up to 78% of the excreted nitrogen and over 50% of the excreted phosphorus and potassium. The greatest losses occurred from housing and storage stages through NH3 emissions (39% of total nitrogen losses) and direct discharge of manure into water bodies or landfill (30–73% of total nutrient losses). There are large differences among animal production systems, where the landless system has the lowest manure recycling. Scenario analyses for the year 2020 suggest that significant reductions of fertilizer use (27–100%) and nutrient losses (27–56%) can be achieved through a combination of prohibiting manure discharge, improving manure collection and storages infrastructures, and improving manure application to cropland. We recommend that current policies and subsidies targeted at the fertilizer industry should shift to reduce the costs of manure storage, transport, and application.