The southern Xinjiang region is close to the desert, and the problem of saline alkali soil is prominent. In order to improve soil physical and chemical properties and increase soil fertility, wood vinegar from the pyrolysis products of cotton stalks was prepared and used to apply organic fertilizer. Through orthogonal experiments, the effects of final temperature, heating rate, and residence time on the yield of crude wood vinegar during the pyrolysis process of cotton stalks were investigated, and corresponding predictive formulas were established. The results show that within the research scope (pyrolysis temperature of 300 ~ 500 ℃, heating rate of 5 ~ 15 ℃/min, residence time of 0.5 ~3 h), the process parameters with the highest yield of crude wood vinegar are pyrolysis temperature of 492 ℃, heating rate of 5.79 ℃/min, and residence time of 0.53 h. Under this parameter, refined wood vinegar and pig manure were mixed in soil to investigate their effects on soil pH, electrical conductivity, organic carbon and other parameters. Normalize soil fertility using the membership degree obtained from weight coefficients and quantile methods, thereby synthesizing various indicators reflecting soil fertility to obtain relative fertility index values. The membership degree was obtained using weight coefficients and quantile methods, and based on this, soil fertility was normalized. Then, various indicators reflecting soil fertility were integrated to obtain the relative fertility value of the soil. The results show that the application of cotton stem wood vinegar combined with organic fertilizer can significantly improve soil conductivity, pH, organic carbon, nitrogen, and phosphorus content. Compared with the control group that only applied organic fertilizer, soil fertility can be effectively restored after crop maturity. In the fifth month of the experiment, the treatment group with added wood vinegar showed a 18.05% increase in relative fertility compared to the control group.