The invention discloses a naphthaquinone compound derived from marine microbes, and a preparation method and application thereof. The systematic name of the compound is 1,2,3,4-tetrahydro-1,2,5-trihydroxy-6,7-dimethoxy-3-methyl-9,10-anthracenone, and the structure is disclosed as Formula (I). The naphthaquinone compound can be continuously obtained by fermentation. The compound has the advantages of high antineoplastic activity, environment friendliness and low use cost, and can be used for preparing antineoplastic drugs. The active naphthaquinone compound derived from microbes is small in amount and simple in structure, and can be used as a precursor of antineoplastic drugs; the structural modification and reconstruction on the basis of the prior art enhance the antineoplastic targeting property and efficiency; and when being used for developing drugs for treating human stomach cancer, human lung cancer, mouse melanoma, human mammary cancer, human pancreatic cancer, human cervical carcinoma, human osteogenic sarcoma, human liver cancer, human colon cancer and human laryngocarcinoma, the naphthaquinone compound has wide application prospects.