Intensive aquaculture is generally characterized by the addition of nutritionally enriched diets. High-protein feed inputs thus lead to an inefficient use of nitrogen, and the waste of the natural resources, mostly fishmeal, from which this nitrogen originated. With increasing concentration, ammonia and nitrite can be toxic to aquatic life. Previous studies demonstrated that Houttuynia cordata floating bed could significantly reduce ammonia and nitrogen (N) in tilapia intensive aquaculture, but little information is available about the effective planting density or proportion of H. cordata and its effects on water quality and microbiota in tilapia co-culturing pond system. For this, this study constructed two aquaponic models (M1 and M2) based on H. cordata and tilapia, and respectively investigated their effects on water quality and bacterial microbiota in the tilapia intestinal tract and the pond water system. The M1 model included four density treatments (350 g/m², 450 g/m², 600 g/m², and 0 g/m²): the control 0 g/m² (no H. cordata floating bed), treatment 350 g/m² (planting 350 g H. cordata per square meter pond water), treatment 450 g/m², and treatment 600 g/m². The M2 model included four cover ratio treatments: the control 0 % (with no H. cordata floating bed), treatment 5 % (growing 5% H. cordata with floating bed), treatment 10%, and treatment 15%. Results showed in the M1 model the water quality trends based on chemical oxygen demand (COD), ammonia nitrogen(NH₄⁺-N), nitrite nitrogen (NO₂^--N), nitrate nitrogen (NO₃^--N), total nitrogen (TN), total phosphorus (TP) and ortho phosphate (PO₄^3–-P) in treatment groups were significantly lower than those in the control groups. And in the three experimental months, the effect of treatment 450 g/m² was relatively more stable than treatments 350 g/m² and 600 g/m². High-throughput sequencing analysis based on α-diversity indices (Chao1, ACE, Shannon and Simpson) showed different H. cordata floating bed treatments (350 g/m², 450 g/m², and 600 g/m²) could significantly improve the bacterial microbiota composition and increase the bacterial microbiota diversity. And these effects were more obvious along with the extension of co-cultured time. In same month, the effects of treatments 450 g/m² and 350 g/m² (P<0.05) were more stable than that of treatment 600 g/m² (P>0.05). Among different months, the effect from seasonal variation on bacterial composition of fish gut or water was greater than the effect from H. cordata floating bed. In the M2 model, results showed that the H. cordata floating bed with different cover ratios could effectively improve the pond water quality and increase the bacterial community richness and diversity in tilapia ponds and fish guts. And the effect of treatment 10% was relatively more stable. These results demonstrated that using H. cordata floating beds in aquaponics could improve the pond water quality and increase the richness and diversity of the bacterial community in tilapia ponds and in fish guts. In this study, the density 450 g/m² was more stable than densities of 350 g/m² and 600 g/m², and a 10% cover ratio of H. cordata floating bed was superior to ratios of 15% and 5%. These results provide a scientific basis for the application of aquaponics based on H. cordata and tilapia.