Anthropogenic activities like overfishing, urban and industrial developments, and coastal pollution are some of the stressors affecting the marine environment. Thermal pollution from coastal industries like power plants represents the main cause of increased temperatures in water bodies, which can affect the marine community structure and function. The aim of this study was: 1) to compare the epifaunal communities associated with three different types of microhabitats: articulated coralline algae around coral colonies (CWC), articulated coralline algae in the absence of coral colonies and other benthic organisms (CNB), and the seaweed Ecklonia cava (ECK); and 2) to determine the potential changes in epifaunal communities in acute response to the increased water temperature resulting from coastal power plant activities in Jeju Island, South Korea. Our findings revealed a strong association between epifaunal abundance and microhabitat type, with CNB exhibiting the highest abundance while ECK showed the lowest. Additionally, an increase in temperature of 0.5–1.5 °C was observed to not alter the overall abundance of epifauna at the impact site, however, it did lead to a shift in the community composition. There was a notable decline in the abundance of amphipods-caprellids, polychaetes, gastropods, and bivalves with their densities nearly halving in response to thermal stress. Furthermore, there was a shift in dominant taxa, transitioning from amphipods-caprellids to amphipods-non-caprellids. Conversely, other taxonomic groups such as isopods and copepods showed a remarkable surge in abundance following the temperature rise. These findings highlight the relationship between rising temperatures and epifaunal community composition while emphasizing taxa’s different responses to thermal stress.