Rice-fish co-culture system (RFCS) is an eco-friendly agricultural mode, but traditional RFCS has revealed many deficiencies. In this study, we constructed a new system of ex-situ rice-fish co-culture (ESRF) and evaluated its performance in ecological advantages. Chemical environmental factors, plankton and microorganisms, as well as ecology and economic benefits, were analyzed in the ESRF system. Results showed that 23.6% fertilizer and 47.5% water were saved in ESRF compared with rice monoculture. After wastewater in the fish ponds flowed through the paddy fields, the concentrations of TN, TP, CODMn, NH4+-N, NO2−-N and DIP decreased 72.78%, 63.81%, 53.32%, 45.54%, 51.31% and 44.05%, respectively through the absorption by rice. The phytoplankton abundance of cyanobacteria in wastewater, mainly Microcystis and Merismopedia tenuissima decreased significantly in ESRF system in July. Rotifer was the most dominant zooplankton in all samples and its abundance decreased significantly in ESRF system. After the aquaculture wastewater flowed through the paddy fields, the relative abundance of several bacteria with the ability of transforming nitrogen and phosphorus increased, such as Vogesella, Comamonadaceae, Flavobacterium, Sphingobium, Brevundimonas and Sphingomonas. These results suggest that ESRF is an eco-friendly and economical agricultural production mode and worthy of application in agriculture production.