The sustainability of intensification of rice production is a prime concern for China. Application of organic amendments, changes in crop rotation system, ducklings' introduction, and construction of vegetated drainage ditches are some of the original management strategies to mitigate environmental pollution from paddy fields. Although these practices affect the rice culturing system through different mechanisms, there is limited investigation on their effectiveness on nutrient pollution alleviation. Therefore, a field study was carried out with the assessment of soil physico-chemical properties, greenhouse gas emissions, nitrogen removal efficiency, grain yield, and economic benefits by comparing the eco-rice culturing system (ER) to the local single rice cultivation system (CK). Results showed that the ER system can significantly improve soil fertility by increasing the pH in acidic soil, organic matter, total nitrogen (TN), and available potassium (K) content by 5.2%, 25.7%, 19.1%, and 19.4% in relation to CK, respectively. Meanwhile, about 10% of the total fertilizer N was removed from the harvesting of the plant species (Myriophyllum elatinoides and Pennisetum purpureum) in the vegetated drainage ditches. However, the ER system decreased the plant height (1.1%) and the number of tillers (9.6%), resulting in a reduction of the total grain yield (6.0%). Moreover, compared with the CK system, the ER system increased CH 4 cumulative emission, global warming potential (GWP), and greenhouse gas intensity (GHGI) by 11.1%, 8.1%, and 14.3%, respectively, and decreased N 2 O by 27.2%, but not statistical significantly (p < 0.05). Even so, by taking the costs of farm operations and carbon costs of greenhouse gas emissions, the net economic benefits by applying the ER system were higher relative to the CK system. Thus, our study provides further understanding of the technology which has the potential to transform sustainable rice production to a more profitable, income generating, and environmentally friendly industry in China.