High-throughput determination of circadian rhythms in metabolic response and their divergent patterns in various microhabitats are crucial for understanding how organisms respond to environmental stresses. A mid-intertidal limpet Cellana toreuma was collected at various time points across both daytime and nighttime in winter during low tide for investigating the diurnal metabolomic responses to cold stress and elucidating the divergent metabolic responses to temperature variations across microhabitats. Temperatures of emergent rock microhabitats were lower than the tidal pool and even aggravated at night. A series of metabolomic responses exhibited coordinated diurnal changes in winter. Metabolic responses which were associated with cellular stress responses and energy metabolism of emergent rock microhabitat individuals were highly induced compared to the tidal pool ones. This study shed lighton the diurnal patterns of metabolomic responses of intertidal molluscs in the field and emphasized the variations in metabolic responses between microhabitats.