Aims <p>Improving the functionality of saline-alkali lands and mitigating the emissions of microbial greenhouse gas (GHG) are crucial for enhancing soil C storage in terrestrial ecosystems. Peat addition and phytoremediation are considered effective strategies for saline-alkali land remediation, but the underlying interactive effects on carbon dioxide (CO₂) and nitrous oxide (N₂O) emissions remain unclear.</p> Methods <p>We assessed the effects of peat amendments at two levels (6&#xa0;g/kg, 18&#xa0;g/kg) in combination with two halophytic plants (<i>Suaeda salsa</i> as a pioneer species that may improves soil structure and reduces salinity, <i>Suaeda glauca</i> as an indicator species tolerant of salt stress and associated with nutrient accumulation). We then measured changes in soil and microbial properties, and thus CO₂ and N₂O emissions.</p> Results <p>Peat amendments and halophytes significantly influenced soil properties, fungal community composition and bacterial diversity. Peat addition with low-concentration significantly inhibited CO₂ emissions in <i>S. salsa</i>, with bacterial alpha diversity and ammonium N content positively correlated with this inhibition, while fungal community composition had a negative effect. In contrast, peat addition had no significant effect on CO₂ emissions in <i>S. glauca</i>. Peat additions at both low and high-concentration significantly increased N₂O emissions in <i>S. salsa</i>, with positive correlation to soil total C/N, dissolved organic C/total dissolved N, and nitrate N. In contrast, peat addition had no significant effect on N₂O emissions in <i>S. glauca</i>.</p> Conclusions <p>Peat additions-mediated GHG emissions depend on halophytes-specific responses. Compared with the <i>S. glauca</i>, peat addition to the pioneer plant <i>S. salsa</i> significantly reduced CO₂ emissions, yet increased N₂O emissions, providing a framework for optimizing peat–halophyte combinations to mitigate GHG emissions.</p>