Abstract: To scientifically evaluate the variation characteristics of energy flux and the carbon sequestration capacity of a winter wheat and one-season rice rotation farmland ecosystem on the coast of East China, we collected flux observations in winter wheat and one-season rice rotation farmland from a vorticity field observation experiment throughout the growth period from 2019 to 2020. We used the flux data processing software of American LI-COR Company to control the data quality and obtained a set of 30 min data sequences. After quality control, carbon sequestration of rice and wheat and its environmental impact factors and multi-time scale variation characteristics of solar net radiation (R_n), latent heat flux (LE), sensible heat flux (H), soil heat flux (G), and CO₂ flux (F_C) were studied and analyzed using energy balance and statistical methods. The results showed that the energy balance ratio of the effective energy and turbulent flux was 0.80, which indicated a high energy closure and reliable flux observations. The variations in monthly LE and R_n over the year showed an “inverted U” distribution, and these two variations were synchronous. The peak value mainly occurred from May to August, and the valley value mainly appeared from January to February and November to December. The fluctuation magnitudes of H and G were significantly lower than those of LE and R_n. Hourly F_C during the day presented a “U-shaped” single peak quadratic curve, thereby indicating that CO₂ was generally absorbed during the day and discharged at night. The daily absorption peak of CO₂ mainly occurred during 10:00–12:30. Daily and monthly F_C generally showed “W-type” variation characteristics throughout the year. The annual carbon emission periods were mainly concentrated in January, June, November, and December, whereas the rest of the year was classified as a carbon absorption period. The absorption peaks were at the jointing and booting stages of winter wheat (March to April) and rice (August). The carbon sequestration during the growth period of winter wheat from February to May was 387.4 g(C)∙m⁻² and 382.2 g(C)∙m⁻² in 2019 and 2020, respectively. Carbon sequestration during the growth period of rice from July to October was 678.2 g(C)∙m⁻² and 599.7 g(C)∙m⁻² in 2019 and 2020, respectively. During the day, when the air temperature increased, the CO₂ absorption capacity of winter wheat and rice increased; however, this absorption trend decreased when the difference in saturated water vapor pressure was greater than 1.7 kPa. The absorption capacity of CO₂ at night was mainly affected by temperature. The capacity of carbon absorption revealed clear diurnal and seasonal variations in coastal winter wheat and rice rotation farmland ecosystems. Considering the annual carbon balance, this ecosystem is a carbon sink. Moreover, it is a robust carbon sequestration area.