The present invention discloses a method for eliminating host DNA contamination for use in viral metagenomic analysis of water environment, belongs to the field of biotechnology, and aims to solve theproblem of a small amount of host cells in a virus concentrate affect sequencing results in the viral metagenomic research of the water environment. The method for viral metagenomic analysis of the water environment is as follows: 1, filtering a water sample through gauze, removing bacteria by a filter column of a filtration system, concentrating, centrifuging, and preparing a virus particle ultra-speed-centrifuge concentrate; 2, adding DNase and RNase working solutions, performing PCR amplification, detecting whether digestion is complete, if the digestion is not complete, adding lysozyme tolyse bacterial cells, continuing digestion, and inactivating nuclease at high temperature to obtain a virus particle concentrate without host genetic material contamination; and 3, amplifying virus whole genome. The sample is treated by the lysozyme for release of DNA of the contaminated bacterial cells, then the DNA is digested by the nuclease, and the operation is simple, and the applicabilityis strong.