The invention discloses a harmless separation system for bone, meat and grease of livestock dying of diseases. The system comprises a dead livestock treatment unit, a pyrohydrolysis and drying unit, a grease pressing unit and a grease purification and separation unit. The dead livestock handling unit comprises a dead livestock sterilizing device and a low-temperature cold storage pool, the pyrohydrolysis and drying unit comprises a high-temperature and high-pressure hydrolysis drying all-in-one machine and a heating plant, the grease pressing unit is a grease press, and the grease purification and separation unit comprises a heating grease storage tank, a heating device, a horizontal centrifuge, a grease settling tank, a first finished product grease tank and a second finished product grease tank, wherein the heating device, the horizontal centrifuge, the grease settling tank, the first finished product grease tank and the second finished product grease tank are arranged at the lower end of the heating grease storage tank. According to the system, the technical problems that due to the fact that the livestock with diseases flow into the market, the environment is polluted, and in the harmless treatment process, resources are wasted, and the treatment cost is high are solved, the investment cost of harmless treatment of the livestock with the diseases is reduced, effective recycling of the resources is achieved, the enterprise economic benefits are improved, meanwhile, the biological environment is effectively protected, and the solid foundation is established for harmless treatment of the livestock dying of diseases.