A high level of antioxidants in organic-produced vegetables has been attributed to soil conditions; however, little is known about the relationships between antioxidants and rhizobacteria under different fertilization treatments. A pot trial for pakchoi (Brassica campestris ssp. chinensis L.) was conducted under greenhouse conditions with: (1) control; (2) chemical fertilizer; and (3) organic fertilizer. The responses of the plant, soil properties, and rhizobacterial community were measured after 45 days of cultivation. Fertilization increased soil nutrient levels and pakchoi productivity and the reshaped rhizobacterial community structure, while no differences in rhizobacterial abundance and total diversity were observed. Generally, most plant antioxidants were negatively correlated with inorganic nitrogen (N) and positively correlated to organic N in soil. The genera of Arthrospira and Acutodesmus contained differential rhizobacteria under chemical fertilizer treatment, which are known as copiotrophs. In addition, the addition of a chemical fertilizer may stimulate organic substance turnover by the enrichment of organic compound degraders (e.g., Microbacterium and Chitinophaga) and the promotion of predicted functional pathways involved in energy metabolism. Several beneficial rhizobacteria were associated with organic fertilizer amended rhizosphere including the genera Bacillus, Mycobacterium, Actinomycetospora, and Frankia. Furthermore, Bacillus spp. were positively correlated with plant biomass and phenolic acid. Moreover, predictive functional profiles of the rhizobacterial community involved in amino acid metabolism and lipid metabolism were significantly increased under organic fertilization, which were positively correlated with plant antioxidant activity. Overall, our study suggests that the short-term application of chemical and organic fertilizers reshapes the rhizobacterial community structure, and such changes might contribute to the plant’s performance.