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Mangrove soils have been recognized as sources of greenhouse gases, but the atmospheric fluxes are poorly characterized, and their adverse warming effect has rarely been considered with respect to the potential contribution of mangrove wetlands to climate change mitigation. The current study balanced the warming effect of soil greenhouse gas emissions with the plant carbon dioxide (CO₂) sequestration rate derived from the plants' net primary production in a productive mangrove wetland in South China to assess the role of mangrove wetlands in reducing the atmospheric warming effect. Soil characteristics were also studied in the summer to examine their relationships with gas fluxes. The soil to atmosphere fluxes of nitrous oxide (N₂O), methane (CH₄) and CO₂ ranged from −1.6 to 50.0 μg m⁻² h⁻¹, from −1.4 to 5360.1 μg m⁻² h⁻¹ and from −31 to 512 mg m⁻² h⁻¹, respectively, which indicated that the mangrove soils act as sources of greenhouse gases in this area. The gas fluxes were higher in summer than in the cold seasons and were variable across mangrove sites. Gas fluxes in summer were positively correlated with the soil organic carbon, total nitrogen, and ammonia contents. The mangrove plants sequestered a considerable amount of atmospheric CO₂ at rates varying from 3652 to 7420 g CO₂ m⁻² yr⁻¹. The ecosystem acted as a source of CH₄ and N₂O gases but was a more intense CO₂ sink. However, the warming effect of soil gas emissions accounted for 9.3–32.7% of the plant CO₂ sequestration rate, partially reducing the benefit of mangrove plants, and the two trace gases comprised 9.7–33.2% of the total warming effect. We therefore propose that an assessment of the reduction of atmospheric warming effects by a mangrove ecosystem should consider both soil greenhouse gas emissions and plant CO₂ sequestration.