Ecological floating beds are widely used as an economic and environmentally friendly technology for the treatment of black smelly water bodies, while their treatment capacity is limited by the plant root area and the depth of plants reaching the water body. In this study, the enhancement effects and microbial mechanism of different fillers on the treatment capacity of ecological floating beds were investigated by constructing ecological floating beds with interspecies of Myriophyllum aquaticum and Iris sibirica plants through suspension balls, biological ropes, elastic and combined fillers respectively. Furthermore, the optimal addition of selected filter and its kinetic model of pollutant removal from the floating bed was investigated. The results showed that the best removal rates of COD, ammonia nitrogen, and total phosphorus are >99%, 43.85%, and 14.03%, respectively. The highest microbial abundance, the most uniform species composition distribution and the highest microbial diversity on the surface of the bio-rope filler have been observed, and the bio-rope filler can enrich nitrogen and phosphorus removal functional bacteria such as Flavobacterium, Exiguobacterium, Chryseobacterium, Microbacterium and Caulobacter. 12.5 m/m3 is the best amount of bio-rope filler for the remediation of mild black smelly water bodies, and the corresponding removal rates of COD, ammonia nitrogen, and total phosphorus are respectively 96.4%, 38.5%, and 56.6%. The kinetic model fitting revealed that the primary kinetic model could better fit the ammonia nitrogen and COD degradation patterns of bio-rope-enhanced ecological floating bed. The results of this study can provide reference for the subsequent research and application of ecological floating bed enhancement.