In order to explore the differences in soil greenhouse gas emissions between Shihezi Irrigation Area, Xinhuzongchang Irrigation Area and Mosowan Irrigation Area, through long-term field observation and sample collection, adopts the static closed chamber-GC technique, daily observation was conducted to observe the soil greenhouse gases in Shihezi Irrigation District, Xinhuzongchang Irrigation Area and Mosowan Irrigation Area of Manas River Basin in 2019 at the seedling stage, flowering boll stage and spitting stage, and statistical methods were applied, and combined with soil temperature, water content, pH, organic carbon, ammonium nitrogen, nitrate nitrogen and other factors in the Manas River Basin. The results showed that: (1) Soil CO₂ and N₂O had obvious seasonal and daily changes, and the peak of soil CO₂ and N₂O emission fluxes appeared at the flowering boll stage, which were 527.160 and 1.713 mg/(m²·h). At the same time, the peak of the daily change of CO₂ emission flux appeared at 13:00, and the daily change peak of N₂O emission flux appeared at 17:00, which was manifested as a unipolar curve. The emission fluxes of the two soil greenhouse gases during the growth period were different between different irrigation areas, showing the irrigation area of Xinhuzongchang > Mosuowan> Shihezi. (2) Soil CO₂ and N₂O emission fluxes were more significantly affected by temperature, and soil CO₂ and N₂O were significantly positively correlated with temperature. The Q₁₀ of Shihezi Irrigation District, Xinhuzongchang Irrigation District and Mosowan Irrigation District were 1.31~1.82, 1.40~2.68 and 1.32~1.92, respectively. (3) The carbon reservoir reserves of cotton in Shihezi Irrigation District, Xinhuzongchang Irrigation Area and Mosowan Irrigation District were 3.34, 2.93 and 2.8 Tg, respectively.