This study aimed to evaluate the feasibility of Biofloc technology (BFT) in Carassius auratusvar. Pengze aquaculture and to investigate the effects of total suspended solids (TSS) concentration on the growth of Pengze crucian carp, its intestinal tract, and the microbial community structure in the aquaculture water. The experiment included four TSS concentration groups: BF300, BF500, BF700, and BF900, as well as a water-exchanged control group (CW), and the Pengze crucian carp were cultured for 120 days. The results showed that the total ammonia nitrogen and nitrite nitrogen in the water of the Biofloc treatment groups could be maintained at low levels. The highest weight gain rate, body condition, specific growth rate, and condition factor were observed in the BF500 group, which also had the lowest feed coefficient of 1.42. In addition, there was no significant difference in the content of T-SOD and LSZ among the groups (P > 0.05). Microbiome analysis showed that the richness index of the intestinal microbial community in the Biofloc group decreased with the increase of TSS concentration in Pengze crucian carp; the dominant bacterial phylum in the intestine was Proteobacteria, Bacteroidota, Fusobacteriota, and Actinobacteriota, with Proteobacteria being the main bacterial group. The dominant bacterial phylum in the aquaculture water of the Biofloc group was Proteobacteria, Bacteroidota, Chloroflexi, and Actinobacteriota. In summary, the optimal TSS concentration for Pengze crucian carp was 500 mg/L, and BFT can serve as a new model for the green aquaculture of Pengze crucian carp.