Land degradation severely affects soil functions, thereby weakening crop productivity. However, the quantitative effects of the soil organic matter (SOM) composition and soil microbial properties on maize yield remain unclear under different levels of land degradation. Here, a gradient of land degradation was selected for sampling in the Horqin Sandy Land in northeast China. The results show that the relative abundances of aliphatic and aromatic groups decreased by 21.51% and 86.01% with increasing land degradation, respectively, and the considerable increase in polysaccharide groups led to a decrease in stability and resistance to SOM decomposition. Microbial properties, such as microbial biomass carbon, basic respiration, qCO2, and enzyme activities, decreased as a result of land degradation. The phospholipid fatty acid content and the ratio between bacteria and fungi markedly decreased with an increasing level of land degradation, and the ratio of G+ to G− markedly increased. Correlation analysis confirmed that the microbial properties were significantly related to the SOM composition, and the random forest model indicated that fungi were key factors affecting maize yield (7.15%, p < 0.05). Moreover, the results of the structure equation modelling revealed that land degradation reduced the soil physiochemical properties, resulting in a decrease in microorganisms, causing variations in the SOM composition and directly leading to a decrease in crop yield. The effect of microorganisms (β = 0.84 ***) on maize yield was greater than that of the SOM composition (β = 0.53 **). Our investigation can provide a theoretical basis for the conservation of the cropland in Horqin Sandy Land.
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