The invention provides Xanthone compounds and a preparation method thereof, and application of the Xanthone compounds in the field of agriculture, belonging to the field of fungus extracts. A fermentation extract is obtained from Aspergillus versicolor D5 derived from ocean, and 15 compounds are obtained through separation and extraction, wherein 6 compounds are identified as new compounds, and 9compounds are identified as known compounds. The resuts of herbicidal activity tests and antifungal activity tests show that the Xanthone compounds have good antifungal and herbicidal activity, are environment-friendly, safe and efficient, and have better or equivalent control effects compared with chemical pesticides.