To investigate the effects of combined application of biochar and microbial fertilizer on greenhouse gas emissions and sunflower yield in saline-alkali soil under plastic film mulching and drip irrigation. Field experiments were conducted in saline-alkali soil in the Hetao Irrigation Area of Inner Mongolia, with different combinations of biochar (0, 7.5, 15 t/hm2) and microbial fertilizer (0, 112.5, 225 kg/hm2). Greenhouse gas emissions were monitored using static chamber-gas chromatography method. Changes in soil physicochemical properties, global warming potential (GWP), and sunflower yield were analyzed. The results showed that: (1) Compared with the control treatment (0 t/hm2 biochar + 0 kg/hm2 microbial fertilizer), the treatment of 7.5 t/hm2 biochar + 225 kg/hm2 microbial fertilizer increased soil organic carbon, available phosphorus, and available potassium contents by 63.9%, 155.7%, and 46.8%, respectively. (2) Compared to the control treatment, the treatment with 7.5 t/hm2 biochar + 225 kg/hm2 microbial fertilizer reduced cumulative CO2 emissions from 4373 kg/hm2 to -394.3 kg/hm2, increased cumulative CH4 emissions from -0.08 kg/hm2 to 0.1 kg/hm2, reduced cumulative N2O emissions from 0.23 kg/hm2 to -0.09 kg/hm2, and decreased GWP from 4438.3 kg/hm2 to -417.2 kg/hm2. (3) Under the treatment of 15 t/hm2 biochar + 225 kg/hm2 microbial fertilizer, sunflower yield reached 4137.5 kg/hm2, increased by 39.4% compared with the control treatment (2968 kg/hm2). (4) Mantel test analysis revealed that sunflower yield was extremely significantly correlated with soil physicochemical properties (p < 0.01); CO2 emissions were significantly correlated with ammonium nitrogen and moisture content, N2O emissions were significantly correlated with nitrate nitrogen, and CH4 emissions were extremely significantly correlated with nitrate nitrogen (p < 0.05). The combined application of biochar and microbial fertilizer can simultaneously improve saline-alkali soil, reduce greenhouse gas emissions, and increase sunflower yield, with 7.5 t/hm2 biochar + 225 kg/hm2 microbial fertilizer being the optimal combination. This technique provides a new strategy for reducing greenhouse gas emissions and increasing crop yields in saline-alkali agricultural production.