Biodiversity in paddy ecosystems not only enhances crop production but also regulates ecosystem functions, providing various ecosystem services. Benthic macroinvertebrates are crucial organisms that play vital roles in these ecological processes; however, research on their community dynamics in paddy ecosystems is still limited. This study aimed to examine how the community characteristics and ecological functions of benthic macroinvertebrates differ across various types of organic floury rice cultivation. The findings indicated that Rice Field 2 (RF2) hosted a greater diversity of species compared to the other paddy fields. Over time, both the diversity and richness indices in RF2 and RF3 were significantly higher than those in RF1. Similar trends were observed in the functional feeding groups (FFGs) and habitat orientation groups (HOGs). These results suggest that organic floury rice cultivation practices and proximity to the Doombeong (traditional farm pond) jointly influence the community composition and ecological functions of benthic macroinvertebrates. Consequently, differences in cultivation practices can alter vegetation structure, while the complex habitat provided by Doombeong serves as an important refuge for benthic macroinvertebrate communities, aiding in biodiversity conservation and the maintenance of ecological functions in paddy ecosystems.