Fengycin is a cyclic lipopeptide with multiple effects, including cell membrane disruption, induction of systemic resistance in plants, and plant growth promotion. This study used a co-culture system to produce fengycin in a sugar mixture fermentation medium simulating lignocellulosic hydrolysate. First, we compared the fengycin production profiles of the pure cultures and co-culture of three Bacillus subtilis, 168DSABA1, BSP003, and BSJ0232, in a sugar mixture fermentation medium. The co-culture system was then optimized (relative inoculation ratio, ratio of glucose to xylose in the sugar mixture, fermentation time, total carbon source concentration and tryptone concentration) using response surface methodology (RSM) based on single-factor experiments, which increased the fengycin titer of the co-culture system from 241.7 ± 12.0–575.5 ± 5.8 mg/L. Finally, metabolomics was used to analyze the reasons for the increase of fengycin production and the deficiencies of the system: Based on this a co-culture system containing four Bacillus subtilis (4BS) and a co-culture system containing five Bacillus subtilis (5BS) were constructed, which further increased the titer of fengycin to 650.2 ± 9.6 mg/L and 2396 ± 42 mg/L, respectively. The present study provides a reference or improving the industrial production of fengycin and the utilization of lignocellulosic hydrolysates.