In plant communities, genotypic diversity can impact the plant community structure and ecosystem functions, but related research has focused on native plants. Therefore, whether genotypic diversity affects the growth of invasive plants and then changes the wetland microecosystem remains unresolved. In this study, six different genotypes of Hydrocotyle vulgaris, a common invasive plant in China, were selected to construct populations with three different genotypic diversity levels (one, three, and six genotype combinations, respectively) to explore the effects of different genotypic diversity levels on the growth and physiological traits of H. vulgaris, and soil nutrients and greenhouse gas emissions of the wetland microecosystem under flooding conditions. We found that genotypic diversity improved the leaf area, root to shoot ratio and photosynthetic physiological traits of H. vulgaris, especially under flooding. Moreover, genotypic diversity increased soil organic matter (SOM) contents in the wetland microecosystem, while it reduced the cumulative nitrous oxide emissions under flooding conditions. Overall, genotype diversity improved photosynthetic traits of H. vulgaris, further increased SOM, and reduced the N2O emissions of the wetland microecosystem. The results of this study can provide a theoretical basis for exploring how genotypic diversity levels affect the invasiveness of invasive plants and ecosystems in wetland microecosystems.