This study applied the static chamber method to evaluate the CO2 fluxes from December 2013 to October 2014 in the coastal wetland of Jiaozhou Bay, China. The study area was divided into Spartina alterniflora flat, Phragmites australis flat, Suaeda salsa flat and mud flat. Results showed that net ecosystem CO2 exchange (NEE) presented obviously temporal and spatial variations during growing season, and slight fluctuation in non-growing season. Vegetated flats (S. alterniflora flat, P. australis flat and S. salsa flat) acted as CO2 sinks during growing season and CO2 sources during non-growing season; while mud flat acted as a CO2 sink through the entire period. Over the growing season, the estimated total NEE were −1202.83 g CO2 m−2 in S. alterniflora flat, −1129.16 g CO2 m−2 in P. australis flat and −237.43 g CO2 m−2 in S. salsa flat, respectively. Daytime NEE were significantly exponential related to light intensity in S. alterniflora flat and P. australis flat; whereas no overt exponential relationship was found between these two factors in S. salsa flat. In P. australis flat, ecosystem respiration (Reco) and gross primary production (GPP) in growing season were estimated to be 2874.05 and 1744.89 g CO2 m−2, respectively; Reco was significantly exponential related to air temperature and soil temperature at different depths, among which soil temperature at the depth of 5 cm was the most remarkable; temperature sensitivity (Q10) of Reco ranged from 2.72 to 3.67. Aboveground biomass of P. australis over the entire growing season showed non-linear relationships with NEE, GPP, and Reco; while it showed significant linear relationships with these three factors during early and peak growing season. As for the mud flat acting as a CO2 sink, it is supposed to be caused by inorganic process, however the mechanism is not definite. Further research on the long-term and complete observations of CO2 exchange at the mud flat-atmosphere interface is necessary.