This study aimed to investigate the adaptability of commercial probiotics to the biofloc system, as well as the influence on bacterial community, water quality and aquatic animal growth. Two biofloc systems nursing Litopenaeus vannamei postlarvae for 28 days were designed, the control (cBFT) and pBFT with addition of commercial probiotics (containing Bacillus, Clostridium, Enterococcus, Lactobacillus and Rhodopseudomonas). Results showed that at the end of the experiment, only the absolute abundance and the proportion of Bacillus contained in commercial probiotics (2.1 ± 0.8 × 105 genome copies mL−1 and 0.12 ± 0.03%) significantly increased in pBFT compared to those in cBFT (1.7 ± 0.8 × 104 genome copies mL−1 and 0.03 ± 0.02%), respectively (P < 0.05). Absolute abundances and proportions of several autochthonal bacterial genera (i.g., Acinetobacter, Anaerospora, Arthrobacter, Devosia, Luteolibacter, Marivita and Mycobacterium) also significantly elevated in pBFT (P < 0.05). Total suspended solids (TSS) and turbidity (415.2 ± 79.6 mg L−1 and 379.0 ± 86.4 NTU) were significantly higher in pBFT than both parameters in cBFT (118.1 ± 23.9 mg L−1 and 109.4 ± 44.3 NTU), respectively (P < 0.05). Whereas, zootechnical indices (except survival rate) were significantly lower in pBFT than those in cBFT, respectively (P < 0.05). The integrated impact model of commercial probiotics explained 57.9%–77.1% variations of shrimp growth performance, and showed that commercial probiotics as well as some autochthonal bacteria positively correlated with turbidity which in turn negatively correlated with zootechnical indices (P < 0.05). The findings suggested that added probiotics (especially Bacillus) induced changes on the autochthonal bacterial community, leading to changes of water quality which consequently resulted in the depression of growth performance of shrimp.