It has been reported that supplying a carbon source and probiotics improves water quality and animals in aquaculture systems. Most studies used molasses as a carbon source, which is a mixture of carbohydrate, fat, and protein. In the present study, sucrose and probiotics (Bacillus licheniformis; hereafter referred to by only the genus name “Bacillus”) were added in the culture media of 5‐d‐old postlarvae of whiteleg shrimp Litopenaeus vannamei and then cultured for 20 d. The results showed that compared with the control concentrations of NH4+‐N, NO2−‐N, and NO3−‐N, values were lower in treatments with sucrose and Bacillus, suggesting that water quality was improved and material circulation was promoted. Values of dissolved oxygen decreased, probably due to oxygen consumption during microbial growth and oxidation processes. Body length growth rate of whiteleg shrimp was significantly higher in treatments with sucrose and Bacillus compared with the control, which might result from an increased energy uptake from ingesting microorganisms. In comparison to the control, treatments with sucrose and Bacillus greatly influenced bacterial community structure. Among them, the proportion of Actinobacteria increased and that of Proteobacteria decreased. Actinomycetes can degrade organic compounds and produce a wide variety of antibiotics, vitamins, and enzymes, inhibiting growth of some pathogenic microorganisms. Proteobacteria includes many pathogenic bacteria. Changes in these two phyla suggest that the immunity of whiteleg shrimp might be enhanced in response to treatments. These results indicate that microorganism composition might be important to biofloc systems. Further investigations in this area would help guide aquaculture production.