As a common food processing technology, microbial fermentation is becoming increasingly popular to promote the bioactivity of materials. This study aims to enhance rape bee pollen bioactivity through fermentation and trace the potential components associated with its bioactivity. The antioxidant and anti-inflammatory activities of unfermented bee pollen and fermented bee pollen were evaluated, and their correlation with differential metabolites was analyzed. The results indicated that fermentation significantly (p < 0.05) improved the antioxidant (>2.3-fold) and anti-inflammatory (>1.36-fold) activities of bee pollen, and increased the contents of total phenolics and flavonoids by 1.99 and 1.53 folds. Moreover, the correlation analysis results indicated that 15 components, including three phenolamides, one flavonoid aglycone, seven fatty acids, three amino acids and one ketone compound, were positively correlated with bee pollen antioxidant and anti-inflammatory activities. These results suggest that fermentation is a promising approach to increase the bioactivity of bee pollen.