Soil is an extremely significant resource for human survival, and agglomerates, as the basic unit of soil structure, not only enhance soil fertility and control the biological validity of nutrients, but also strengthen the soil's erosion resistance. The mass application of fertilizers may have a significant impact on crop growth and soil structure, and the rational application and dispensing of fertilizers will be an urgent issue to be addressed. Therefore, the effect of fertilizer application on the stability of water-stable soil aggregates needs to be studied under different meteorological and soil conditions to draw more general and feasible conclusions. Our Meta-analysis of data from 220 of 56 published studies found that fertilizer application increased mean weight diameter (MWD) by an average of 18% compared to the no-fertilizer treatment. Among the nitrogen (N), phosphate (P), and organic (OM) fertilizer treatments, the organic fertilizer treatment had a greater stimulatory effect on MWD (26%). Among the different fertilizer levels, low level of phosphorus (<40kg·hm-2·yr-1), high level of N (>120kg·hm-2·yr-1), and low level of organic fertilizer (<5000kg·hm-2·yr-1) increased MWD by 19%, 14%, and 41% respectively. Across soil types and land use types, the response to MWD was positive for red soils and paddy fields, and the stimulatory effect of organic fertilizer was more significant compared to chemical fertilizer. The regression model showed that the response ratio of MWD was negatively correlated with the response ratio of soil pH and bulk density (BD), and positively correlated with the response ratio of soil organic carbon (SOC) and microbial mass carbon (MBC). Meanwhile, the PLS-SEM model showed that average annual temperature was the main factor affecting the stability of soil aggregates, and the average annual rainfall is the secondary factor. Therefore, this study found that the long-term use of organic fertilizers in place of some chemical fertilizers was more effective than chemical fertilizer alone. Temperature and rainfall have greater effects on the response of fertilizer to soil aggregate stability.