Controlling mechanism of air-sea carbon flux in estuary-shelf continuum is important for understanding the role of ocean in “carbon neutrality” goal of China. Based on underway sea surface partial pressure of CO2 (pCO2), temperature and salinity in the Changjiang (Yangtze River) Estuary-East China Sea in spring of 2017, the spatial variations of pCO2 in four domains of the Changjiang Estuary-East China Sea continuum were presented. The roles of water mass sources, organic matter production and decomposition in controlling pCO2 were discussed semi-quantitatively. The results indicated that water mass sources were key factors in determining pCO2 and air-sea carbon flux in the Changjiang Estuary-East China Sea continuum. In addition, production and decomposition of organic matters also influenced pCO2 significantly. Influenced by Changjiang discharge, surface waters in the inner Changjiang Estuary and Zhejiang coast had relatively high pCO2, served as source of CO2 to atmosphere, with magnitude of 5.36 mmol·m-2·d-1. The north and east of study area were influenced by the Changjiang Diluted Water, and Kuroshio Surface Water, respectively. While, they were both carbon sinks with magnitude of -15.44 mmol·m-2·d-1 in the north study area. The average air-sea carbon flux in study area in spring of 2017 was -6.73 mmol·m-2·d-1. End-member mixing model revealed that decomposition of organic matter increased pCO2 of the inner estuary by about 200 μatm, which transferred the inner estuary from carbon sink to carbon source in spring; the shelf waters were carbon sink if water mass sources were considered only, while biological production decreased pCO2(decreased 144 μatm) further, and enhanced the carbon sink.