Improving the treatment performance of mature surface flow constructed wetlands (SFCWs) is critical for long-term sustainability. Nevertheless, the mechanisms of plant species affecting the treatment performance of mature SFCWs remain largely unexplored. In this study, three 6-year-old field-scale SFCWs were subjected to orthogonal tests, with Nelumbo nucifera, Typha angustifolia, and Zizania latifolia as plant species. The aim was to understand how the emergent plant species selected for the newly constructed wetlands influenced the nitrogen and phosphorus treatment performance at maturity. The results showed that plant species significantly affected total nitrogen (TN) treatment performance through dissolved oxygen and water temperature. Typha and Zizania had larger above-ground biomass and denser canopies than Nelumbo, significantly increasing anaerobic zones and water temperature. Therefore, SFCWs with Typha or Zizania had the best organic nitrogen and nitrate nitrogen treatment performance compared to those with Nelumbo. However, the integrated ability of microbes and plants to remove ammonia nitrogen was not affected by internal factors in mature wetlands. Plant species significantly affected total phosphorus (TP) treatment performance through local flow patterns. Although plant species did not significantly affect general hydraulic performance, Zizania had denser tillers and thicker stalks than Nelumbo and Typha, increasing flow velocity near the wetland bottom. Therefore, SFCWs with Nelumbo or Typha were more capable of TP removal than those with Zizania. Overall, Typha was the optimal plant species compared to Nelumbo and Zizania for efficient removal of TN and TP. Therefore, appropriate plant species for newly constructed wetlands are crucial for enhancing nitrogen and phosphorus treatment performance at maturity. From a long-term perspective, SFCWs should be planted with emergent plants with large above-ground parts and sparse tillers. This study provides a mechanistic understanding of the plant species affecting nitrogen and phosphorus in mature SFCWs.