Understanding the mechanisms and controlling factors of ecosystem CO2 exchange in tidal wetlands is of great benefit for research concerning the global carbon cycle and climate change. In spite of this, the multiple controls of ecosystem-atmosphere CO2 exchange in coastal wetlands subject to subdaily tidal flooding have yet to be adequately addressed. In this study, we investigated the tidal influence on ecosystem CO2 exchange in a Phragmites salt marsh of an intertidal shoal in the Changjiang estuary, based on eddy covariance (EC) measurements. The results revealed that the study area acted as a strong sink for atmospheric CO2 (net ecosystem exchange, NEE = -901 g C m−2) in 2018. Photosynthetically active radiation (PAR), air temperature (Ta), and vapor pressure deficit (VPD) were major drivers of NEE on both diel and multi-day scales. The tides, along with the bio-meteorological variables, strongly affect ecosystem photosynthesis (gross primary production, GPP) and ecosystem respiration (Reco) in the tidal wetland, especially on the multi-day scale. Regardless of which flux partitioning method was utilized, tidal inundation generally imposed inhibitory effects on GPP, which were directly attributed to tidal water level (TWL) and salinity. The daytime data-based estimates of Reco was also suppressed on average under the tidal inundation condition when Ta was higher relative to the non-inundation condition, reflecting the influence of TWL on Reco and the reduced sensitivity of Reco to Ta. We observed that NEE responded positively or negatively to tidal flooding, depending on the magnitude of tidal suppression on GPP and Reco. When Ta was roughly between 28 and 32°C and PAR was > 1200 μmol m−2 s−1, GPP was suppressed by tides more than Reco during the early and rapid vegetative stage, while during the peak vegetative stage, the opposite was true. This study not only shows the unique impact of tidal salt marsh wetlands on carbon uptake, but it also represents an example of a coastal wetland in which tidal inundation promotes the net uptake of CO2.