Coastal ecosystems are recognized as important carbon reservoirs. However, assessments of coastal carbon dioxide (CO2) fluxes often neglect unvegetated tidal flats, particularly in peri-urban areas. This study investigated the gross primary production (GPP), net primary production (NPP), and total respiration (TR) of three tidal flats in Hong Kong, one of the largest cities in South China, during both summer and winter seasons to understand their CO2 fluxes. Results showed that GPP of three tidal flats was significantly higher in winter than in summer. However, no significant seasonal variations in TR were observed among the tidal flats. Structural equation modelling was used to examine the drivers of CO2 fluxes in the three tidal flats. The model showed that temperature and microphytobenthos abundance were identified as positive drivers of GPP, while sediment mud content had a positive effect on TR. The estimated daily NPP of these tidal flats ranged from -0.853 to 0.112 g C m−2 d−1, which is lower than the mean value reported for global vegetated coastal wetlands. Despite some seasonal and spatial variations, those peri-urban tidal flats may be considered as weak CO2 sources rather than CO2 sinks.