The rapid growth of modern animal husbandry in China has supplied meat, eggs, and milk for Chinese residents, meanwhile the rapid transformation to intensive husbandry operations has also produced a large quantity of livestock and poultry manure. However, due to the failure of integration of animal husbandry and crop plantation, most of the livestock and poultry manure has not been treated and utilized, which may cause serious environmental pollution and public health risks. Antibiotics, heavy metals, pathogens, and other pollutants contained in livestock and poultry manure can enter farming soil, surface water, and groundwater during the transportation, storage, processing, and utilization of livestock and poultry manure, contaminate food, and pose direct and indirect risks to human health. Based on published statistics and papers, this article systematically analyzed the main pollutants discharged from livestock and poultry manure, their impacts on the environment, as well as the potential health risks by exposure to these pollutants. Recommendations on how to scientifically utilize animal manure were proposed, aiming to better protect human health.