In order to investigate the effects of bioorganic fertilizer application on the chemistry and microbial characteristics of saline-alkali soil in Ningxia Yellow River Diversion Irrigation Area, and to clarify the optimal application amount and fertilization mode of bio-organic fertilizer, the treatments were included applying bioorganic fertilizer 0 t/hm² (CK), 4.5 t/hm² (T1), 9 t/hm² (T2) 13.5 t/hm² (T3), and 9 t/hm² of bioorganic fertilizer and N 360 kg/hm²of inorganic chemical fertilizers (T4) based on the field positioning experiment for 4 consecutive years, soil nutrient contents, enzyme activities, microbial biomass, microbial community carbon metabolism activities and diversities, and maize yields in saline-alkali soil were determined and compared. The results show that: 1) Application of bioorganic fertilizer can significantly reduce soil pH and total salt content, and soil nutrient contents and soil enzyme activities are increased with the increase of bioorganic fertilizer application, and T4 treatment significantly increases soil available potassium content by 14.73%; 2) Carbon source metabolic activity and diversity index of soil microbial community both are increased with the increase of bio-organic fertilizer application, AWCD value of T3 treatment is 0.84 when cultured for 192 h, and Tukey test analysis shows that Shannon and Mcintosh indices are increased by 10.11% and 62.67%, respectively, compared with CK treatment; 3) With the increase of bioorganic fertilizer application, soil microbial biomass carbon, nitrogen and phosphorus contents are increased by 66.78%, 59.19% and 51.84%, respectively, compared with CK treatment; 4) The application of bioorganic fertilizer can significantly increase corn yield and output value, and among them, T4 treatment has the best corn yield and net income, which are 11 499 kg/hm² and 8 709 yuan/hm², respectively. Thus, the long-term application of bioorganic fertilizer can improve the texture of saline-alkali soil in Ningxia, improve soil quality, increase soil biological activity and corn yield, and the application of bio-organic fertilizer 9.0 t/hm² and inorganic fertilizer N 360 kg/hm² is recommended.