Coastal tidal marsh ecosystem is one of coastal blue carbon ecosystems in world, and has high carbon sequestration capacity per unit area. Measurement on carbon budgets at ecosystem scale is critical for revealing carbon source/sink process and carbon sequestration. However, at present data of simultaneous measurement of net ecosystem exchange of CO₂ (NEE) and methane (CH₄) flux, and further assessment on carbon budgets has been poorly reported. Using transparent static chamber and shading by different refractive rates cloth+CO₂/H₂O gas analyzer/gas chromatograph, we measured the NEE, ecosystem respiration (ER), and CH₄ flux in the brackish Phragmites australis marsh and the Cyperus malaccensis marsh in the Minjiang River estuary. We also fitted the relationship between gross ecosystem exchange (GEE) and photosynthetically active radiation (PAR), ER and air temperature, and then estimated the GEE, NEE, and ER at month and annual scales. Both the NEE and ER demonstrated distinctly seasonal variations. The two marsh ecosystems were atmospheric CO₂ sink in spring, summer, and autumn, however in winter they changed to atmospheric CO₂ sources. The carbon sequestration capacity of the P. australis marsh was significantly higher than that from the C. malaccensis marsh. The CH₄ flux from the P. australis marsh was not different from that from the C. malaccensis marsh. Simultaneously considering the CH₄ flux, we calculated the carbon sequestration capacity of the P. australis marsh and the C. malaccensis marsh at annual scale, which was (5371.52±336.97) g CO₂-eq/m² and (2730.32±503.67) g CO₂-eq/m², respectively. The results suggest that both brackish P. australis marsh and C. malaccensis marsh in the Minjiang River estuary are strong atmospheric carbon sink, and plays an important role in mitigating global warming.