Calanus sinicus, the key zooplankton species in the Yellow Sea, China, over-summers in the Yellow Sea Cold Water Mass (YSCWM). Here, we compared the metabolic rates, morphological characteristics and relative expressions of seven genes associated with molting, gonad development, lipid catabolism and stress tolerance of C. sinicus captured both inside and outside the YSCWM in summer. With a large oil sac, low metabolic rate and suppressed molting development, the C5-stage copepods inside the YSCWM were probably quiescent. The gene expressions revealed differences in physiology between quiescent and active copepods in the two regions. When quiescent, the gene associated with molting [ecdysteroid receptor (EcR)] was down-regulated, while genes related to lipid catabolism (Hydroxyacyl CoA dehydrogenase) and stress tolerance (ferritin) were up-regulated. C5s at the margin of the YSCWM up-regulated EcR expression and this could be in response to the elevated Chl a concentration, suggesting that elevated food condition may serve as a trigger that terminated the over-summering of C. sinicus in the Yellow Sea. In conclusion, this study revealed the physiological processes of quiescent and active C. sinicus via morphological, physiological and molecular methods simultaneously, providing a foundation for future investigations of the mechanisms involved in over-summering in YSCWM.