Livestock manure is one of the main sources of agricultural nonpoint source pollution and poses a great threat to the environment and human health. Sustainable management of manure via recycling is an effective means to tackle the problem. Based on field interviews in China, multiple case studies were employed to investigate alternative manure management systems. Four conclusions arose. First, compost-based systems, product-based systems, substrate-based systems, and biogas-based systems were identified as four main types of manure management systems, with each possessing its success factors and risk factors. The adoption of a system was driven by various factors. Second, market-oriented operation was the dominant operation mechanism of all the manure management systems. Third, compared to direct application of manure to croplands, all the four manure management systems could reduce nitrogen loadings from livestock farms and lower their environmental effects. Among the systems, biogas-based systems could reduce nitrogen loadings to the greatest extent, followed by product-based systems and substrate-based systems, and then by compost-based systems. Lastly, integrated management of manure with mixed recycling systems is imperative for reducing its environmental effects, which can benefit from the increasing role of third-party entities in manure recycling. Policy implications were also discussed.