Fermentation conditions affect pectinase production. Among these conditions, fermentation period is one of the important parameters to be optimized for saving the process costs. However, information regarding whether metabolic regulation plays a role is not available. Here, a Bacillus licheniformis strain DY2 was incubated in submerged fermentation for pectinase production for 48 h. The pectinase activity was assayed every 4 h from 8th h of fermentation. The pectinase activity was low at 8 h, middle at 28 h, and peak at 44 h. Consistently, metabolomics analysis showed that the metabolic shift is related to the fermentation period. The metabolomes exhibited almost of differential metabolites in the enriched metabolic pathways, which were decreased at 28 h and 44 h compared to 8 h in a time-dependent manner. Furthermore, reduced palmitic acid and stearic acid in a time-dependent manner were identified as crucial biomarkers at 48 h. These findings in our work reveal that the reduced fatty acid biosynthesis is required for pectinase yield, which was further demonstrated by addition of inhibitors furfural and triclosan to inhibit pyruvate dehydrogenase and fatty acid biosynthesis, respectively. Our work reveals a potential possibility to elevate pectinase yield through metabolomics modulation.