Flax fiber is an important textile material with excellent antibacterial activity and moisture wicking. Degumming of flax roving is essential in determining flax-fiber quality. Traditional degumming requires a large amount of chemicals to process flax roving. This study aimed to reduce the chemical usage and achieve cleaner production during this process by applying microbial treatment to degum flax roving. Microbial degumming instead of acid pickling and NaClO2-bleaching steps can no longer use H-2 SO4 and NaClO2, and the amount of alkali can be reduced by 50%. By analyzing the compositional changes of the main steps in traditional degumming processes and microbial-treatment sample, the application of Bacillus subtilis HR5 can achieve a good degumming effect. Results of environmental scanning electron microscopy, Fourier-transform infrared spectroscopy, thermogravimetric analysis, and X-ray diffractometry analyses showed that the gum was remarkably reduced, which can be confirmed by the gum components. Overall, the breaking tenacity and antibacterial activity of fibers degummed by microbial treatment were better than those treated by traditional degumming. These findings demonstrated the feasibility of microbial treatment as a solution for flax roving degumming.