Soil is a highly significant resource for human survival, and agglomerates, as the basic unit of the soil structure, not only enhance the soil fertility and control the biological validity of nutrients but also strengthen the soil’s erosion resistance. The mass application of fertilizers may significantly affect crop growth and the 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 independent observations from 56 published studies found that fertilizer application increased the 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 more significant stimulatory effect on the MWD (26%). Among the different fertilizer levels, a low level of phosphorus (120 kg·ha⁻¹·yr⁻¹), and a low level of organic fertilizer (<5000 kg·ha⁻¹·yr⁻¹) increased the MWD by 19%, 14%, and 41%, respectively. Across the soil types and land use types, the response to the MWD was positive for red soils and paddy fields, and the organic fertilizer’s stimulatory effect was more significant than that of the chemical fertilizer. The correlation analysis showed that the response rate of the MWD was negatively correlated with the response rate of the soil pH and bulk density (BD) and positively correlated with the response rate of the soil organic carbon (SOC) and microbial mass carbon (MBC). Meanwhile, the partial least square structural equation model (PLS-SEM) showed that the meteorological factors were the main factors affecting the stability of the soil aggregates, while the secondary factors were the soil’s physical and chemical properties. Therefore, this study found that the long-term use of organic fertilizer instead of partial fertilizer is better than the use of chemical fertilizer alone, while more attention should be paid to the influence of temperature and rainfall on the stability of fertilizer in aggregate soil in the future.