The invention relates to an epicoccum nigrum DB3 bacterial strain as well as a preparation and an application thereof. The preparation method comprises the steps of: 1, placing rotten sea grass in an enrichment culture medium, standing and culturing at room temperature, then coating the enrichment culture medium in a separation culture medium, standing and culturing at a temperature of 30 DEG C for 1-4 days to obtain a wild type flax biological treatment bacterial strain; 2, inoculating the bacterial strain obtained from the step 1 into a flax lignin nutrition culture medium, culturing at a temperature of 28 DEG C for 72 hours; and 3, selecting the bacterial strain with the capacity of degrading the lignin from the flax lignin nutrition culture medium to obtain the epicoccum nigrum DB3 bacterial strain. The epicoccum nigrum DB3 bacterial strain can be applied to a process for preparing spinning flax, hemp, jute or red ramie fibers through peroxide degumming. The epicoccum nigrum DB3 bacterial strain has the characteristics of short growth period, low possibility of being polluted, low treatment cost, mild reaction conditions, strong pollution resistance capacity, good heat-resistant performance, no environment pollution and good quality of the treated fibers. The preparation method has a simple process and is suitable for large-scale industrial production.