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The separation between planting and breeding results in an unbalanced distribution of the regional livestock and poultry manure (RLM) industry, and it has raised great concerns. A holistic analysis and problem-solving scheme using 72 townships as the research point was developed in this study. On the basis of a survey from a typical agricultural region in China, the local characteristics of manure discharge, land use, and crop cultivation were analyzed. The assessment of land carrying capacity and environmental risk assessment was conducted by simulating the nitrogen cycle. Afterwards, optimized livestock breeding strategies and inter-regional transfer and flow scheme of manure nutrients were proposed. The spatial distribution of RLM in terms of pig manure equivalent showed an imbalance of high north–south and low middle, and the nitrogen requirement of crops showed a decreasing trend from north to south. In some townships, the environmental risks were higher than level I, which indicated that pollution existed around large construction sites and water areas in the northwest. The land carrying capacity index calculated at 50% nutrient ratio displayed no overloaded risk, whereas 10–20% nutrient ratio exhibited overloaded risk. Assessments showed that the residual RLM and its nitrogen volume were 151,700 and 3574.64 tons per year, respectively. More than 80% of the study area could be used as a nitrogen nutrient sink area, and only six townships are nitrogen nutrient sources. Therefore, optimizing the allocation of manure nutrients is expected to avoid agricultural contamination from livestock manure. [ABSTRACT FROM AUTHOR]