Paddy field ecosystems are crucial for crop production, biodiversity conservation, and ecosystem services. Although previous studies have examined paddy field biodiversity, few have addressed how the distribution and species richness of vegetation and soil seed banks are regulated. This study investigated the distribution of wetland plants and soil seed banks in paddy fields across diverse habitat types and identified factors influencing their patterns. Surveys revealed that conventional paddy field habitats contained only a few herbicide-tolerant species (e.g., Portulaca oleracea L., Cardamine flexuosa With., and Rorippa palustris (L.) Besser). In contrast, organic paddy field habitats exhibited higher species richness and abundance. Cluster analysis and nonmetric multidimensional scaling demonstrated that soil seed bank distribution differed markedly in paddy field habitats with different farming practices and was influenced by distinct soil factors. These findings highlight the importance of understanding vegetation and soil seed bank dynamics in paddy field ecosystems to support biodiversity conservation and sustainable agriculture.