The invention discloses a magnetic separation water body purification system and a separation and purification method thereof. The system comprises a submersible sewage pump, an electromagnetic flowmeter, a pipeline mixer, a coagulation channel, a magnetic seed reaction chamber, a flocculation reaction chamber, a sedimentation tank, a vertical low temperature ionized water treatment unit, a first booster pump, a second booster pump, a coagulant soaking machine, a flocculant soaking machine, a first electromagnetic diaphragm metering pump, a second electromagnetic diaphragm metering pump, a mortar pump, a sludge shearer, a magnetic drum, a sludge concentration tank, a sludge dehydrator, a filtrate storage tank, a dryer, a biomass carbonization furnace, a cooling device, a sewage pipeline, a circulating water pipeline, a medicating pipeline and a sludge pipeline; the method comprises sewage coagulation, sewage magnetization, sewage flocculation, sewage separation, water body purification, sludge shear, magnetic powder separation, sludge concentration, sludge dehydration, sludge drying, sludge carbonization and biomass carbon collection. Closed ring system design is adopted, and system functions are subjected to coordination control by a series connection-parallel connection process.