Abstract: Microhabitat heterogeneity results in significant variations in the thermal environment on a small spatial scale, leading to different intensities of cold stress during extreme low-temperature events. Investigating variations in body temperature and metabolomic responses of organisms inhabiting different microhabitats emerges as an important task for understanding how organisms respond to more frequent extreme low-temperature events in the face of climate change. In the present study, we measured substrate temperature, air temperature, wind speed, light intensity, and body temperature to evaluate the relative importance of drivers that affect body temperature in different microhabitats, and determined the metabolomic responses of intertidal snails Littorina brevicula and limpets Cellana toreuma from different microhabitats (snail: exposed vs. shaded rock; limpet, rock vs. tidal pool) during extreme low-temperature event in winter. Results showed that microhabitat type, substrate temperature, air temperature, wind speed, and light intensity contribute notably to the body temperatures. During extreme low-temperature events, mollusks collected from different microhabitats exhibited microhabitat-specific metabolomic responses that are associated with cellular stress response, energy metabolism, immune response, nucleotide metabolism, and osmoregulation. These metabolic pathways were highly induced in the more exposed areas (exposed rock for snails and rocky environment for limpets). Notably, in different microhabitats, the metabolites enriched from these pathways showed significant correlations with microclimate environmental variables (i.e., substrate temperature, wind speed, and body temperature). Overall, these findings highlight the importance of microhabitat heterogeneity for intertidal species surviving extreme cold events and are essential for understanding cold adaptation of intertidal species in the context of climate change.