A 55‐day mesocosm experiment was conducted to evaluate the effects of commercial microbial products (Novozymes Pond Protect and Novozymes Pond Plus) and extra carbon (glucose) on water quality and bacterial community in a fish polyculture system. A 2 × 2 layout, including four treatments (non‐supplementation of the microbial products or glucose, adding glucose, adding the microbial products and adding the microbial products and glucose in combination), was established. The microbial products and glucose were added on the 40th day, 46th day and 52th day. Ammonia, nitrite and nitrate reduced in the tanks after glucose addition, while adding the microbial products did not significantly affect ammonia, nitrite, nitrate, reactive phosphate, total nitrogen, total phosphorus, chemical oxygen demand and total organic carbon. Adding the microbial products and glucose affected relative abundance of some bacterial taxa, but did not reshape bacterial community. Non‐positive interactive effect on water quality and bacterial community was detected between the microbial products and glucose. This study reveals that supplementation of the microbial products did not benefit water quality in the fish polyculture system, and glucose addition could reduce ammonia, nitrite and nitrate.