Ecological floating beds are used as a water pollution controlling as well was an environment eco-friendly water treatment method. This technology is more advantageous compared to physical and chemical method. At present, there are a number of studies focusing on theoretical aspects as well as the applicability of ecological floating bed, but these studies mainly focused on plant selection, pollutants removal efficiency and mechanism of removal, however, it has never been studied as a whole microbial system.. Based on the spatial distribution of plants and microbes, the plant-microbial compound ecological floating bed system was set up to study the effect of plant-microbial interaction as a whole as well as individually; the interaction between plant and microbes in compound ecological floating bed, and how they affect each other. The results showed that the compound ecological floating bed was more effective towards the removal of TP (≤90%) whereas the removal rates of TN were 60.3%, 31.2% and 31.1%, in the floating bed, plant floating bed and microbial treatment, respectively. The main reason of effectual pollutant removal was the micro ecosystem formed by plants and microbes in a floating bed reactor.