The invention discloses a decarburization, denitrification and dephosphorization deep treatment system. The decarburization, denitrification and dephosphorization deep treatment system comprises an anaerobic biological filter, a denitrification biological filter, a carburization biological filter and a nitrification biological filter which are connected in sequence, wherein the anaerobic biological filter is provided with a water inlet pipe; the nitrification biological filter is provided with a water outlet pipe. The carburization biological filter is connected to the anaerobic biological filter through a first mixed solution reflowing pipe in a returning manner; the nitrification biological filter is connected to the anaerobic biological filter through a second mixed solution reflowing pipe in the returning manner; the nitrification biological filter is connected to the denitrification biological filter through a nitrification mixed solution reflowing pipe in the returning manner; the water inlet pipe of the anaerobic biological filter is connected to the denitrification biological filter through overstepping the water inlet pipe; the denitrification biological filter is provided with a primary sedimentation output water leading-in pipe connected with output water of a primary sedimentation tank. The system and the method disclosed by the invention are multi-combination, synchronous and interactive type decarburization, denitrification and dephosphorization deep treatment system and method, which have the advantages of high anti-impact load, high partitioning function, high treatment capability, short process flow, small occupied area and good treatment effect.