Purpose <p>Climate warming can cause more frequent droughts in wetlands, leading to changes in soil properties and vegetation expansion, and influencing carbon dioxide (CO₂) emissions. Soil consolidation accelerated by drought is assumed to be an important factor affecting CO₂ emissions from wetland soils. However, very few studies have proved this.</p> Methods <p>Here, we employed a mesocosm experiment to simulate sedge colonization under warming scenarios over an entire growing season. This experiment continuously monitored CO₂ fluxes, along with water vapor (H₂O) fluxes, changes in sediment surface elevation, soil chemical properties, plant growth characteristics, and the diversity of bacterial and fungal communities.</p> Results <p>Warming significantly impacts soil CO₂ emissions in mudflats, causing increases of up to 75%. However, in sedge colonized treatments, an increase of only 8% for soil CO₂ flux was found. In addition to H₂O fluxes in the mudflat, significant differences were only found in sediment surface elevation change between warming and control treatments among all the other factors. A significant positive correlation between CO₂ flux and H₂O flux with sediment surface elevation change was revealed in the mudflat, as opposed to the sedge colonized treatment.</p> Conclusions <p>Our results indicate that soil consolidation caused by drought was the primary driver leading to the higher CO₂ emissions in mudflat under warming conditions, while sedge colonization can offset this effect. This study first provides evidence for the effect of soil consolidation on wetland CO₂ emissions, providing new insights into evaluating CO₂ budgets under global climate change.</p>