Based upon 21 field surveys conducted from March 2011 to November 2013, monthly variation of carbon dioxide partial pressure (pCO2) and other carbon system parameters were investigated for the first time (to our knowledge) at A4HDYD station (38°40′N, 122°10′E) located in the North Yellow Sea, a region with a seasonal thermocline. Surface pCO2 was undersaturated from March to May and nearly in equilibrium with the atmosphere from June to August. During September and November, pCO2 declined to a lower level than that from June to August, but reached the highest level in December. In contrast, pCO2 declined to atmospheric CO2 levels in February. Overall, the study area was a net CO2 sink at a rate of 0.85±0.59molCm−2yr−1. The underlying processes governing the variation of pCO2 were also examined. In general, temperature had an important influence on the monthly variation of pCO2, but its effect was counterbalanced by biological production in spring and vertical mixing in early winter. Our study indicated that dynamic mechanism studies based on high temporal resolution observations are urgently needed to understand the complexity of the carbon cycle and detect biogeochemical changes or ecosystem responses to climate change on continental margins.