As a key component of material cycling and energy flow in Lake Nakaumi, macrobenthos play a vital role in maintaining the stability of the lake ecosystem. However, against the backdrop of global climate change, research on the macrobenthic community in this lake remains insufficient. In particular, the structural changes of this community following the impact of strong El Niño events (2014 to 2016) remain unclear. Therefore, based on macrobenthos monitoring data collected from Lake Nakaumi in 2017 and 2018, a period following the attenuation of the strong El Niño event, this study employs multivariate statistical analysis methods to comprehensively examine the community composition, diversity, ecological niches and interspecific relationships of dominant species, as well as the seasonal differentiation of the macrobenthic community. The main conclusions are as follows: The community consists primarily of 34 species belonging to 6 phyla, with annelids being the most species-rich group. Notably, there are no euryecious species (species with broad niches) within this community. The niche overlap values among dominant species exhibit interannual fluctuations, which may be attributed to the combined effects of benthic habitat fragmentation, spatiotemporal randomness in the distribution of suitable environments and resources, and environmental filtering. Temporally, the community can be distinctly divided into two seasonal groups: the winter-spring group and the summer-autumn group. In terms of diversity, the winter-spring group outperforms the summer-autumn group. This significant dissimilarity is mainly driven by seasonal indicator species and species with density differences between the two groups. Such temporal variations in community composition represent a key mechanism enabling the macrobenthic community in Lake Nakaumi to maintain stability amid extreme seasonal changes.