Peatland is an aquatic-terrestrial transitional ecosystem. Its biological communities (e.g., vegetation) change during the process of swamping exerts significant impacts on carbon burial and peatland development. As an important secondary producer of peatland ecosystems, the change of chironomid community provides key clues for tracing the environmental change and developmental history of peatlands. However, the existing surveys on peatland chironomid communities are limited to peat habitats or open water in peatlands, but rarely carried out along multiple habitat gradients. The Dajiuhu Wetland, located in the Shennongjia Forestry District, encompasses a variety of habitats including peatlands, lakes, and temporary water bodies. In this study, surface sediments and water samples in different habitats were collected. We extracted the subfossil chironomids in the surface sediments to analyze the structural differences of midge community in different habitats. The relationships between the chironomid community and environmental factors were then explored. Our results revealed that: 1) the dominant chironomid taxa varied significantly between different habitats in the Dajiuhu Wetland. Semi-terrestrial taxa, such as Limnophyes, Psilometriocnemus and Pseudosmittia were the dominant taxa in the Sphagnum moss hummocks, while the typical lacustrine species (i.e., Polypedilum nubeculosum-type) dominated the communities in peat lake habitat. Lacustrine and semi-terrestrial taxa coexisted in transitional waters (Sphagnum moss hollows, ditches and ponds); 2) loss-on-ignition, depth to water table and pH were the key environmental factors in shaping chironomid communities in different habitats. Hydrological conditions indirectly influenced the chironomid community compositions primarily through their impacts on other environmental factors such as carbon accumulation process; and 3) the content and type of organic matter changed significantly along the gradient from aquatic to semi-terrestrial habitats, accompanying with the change of chironomid community from the coexistence of lacustrine and semi-terrestrial taxa to the dominance of semi-terrestrial taxa. The chironomid community responded well to habitat change in the Dajiuhu Wetland. This study revealed the differences of chironomid community between different habitats and the potential driving factors. It is expected to provide a scientific basis for future studies on historical peatland development at a long-term scale based on subfossil chironomids.