Fertilizer application can affect the physicochemical properties of soil, such as the contents of large aggregates, humus, and exchangeable cations, thereby influencing soil erosion resistance. However, the rill erosion resistance and its key influencing factors of soil following long-term balanced fertilizer application remains unclear. This study aimed to analyze the change in rill erosion resistance following 44 years of balanced fertilizer application (No changes in the type of fertilizer) to non-calcareous soils and establish a Partial Least Squares Regression (PLSR) model of rill erodibility (kd) and soil critical shear stress (τc) to changes in the physical and chemical properties of the soil. Five treatments were designed: (1) CK (no fertilizer applied), (2) N (nitrogen), (3) NP (nitrogen plus phosphorus), (4) NK (nitrogen plus potassium), and (5) NPK (nitrogen, phosphorus, and potassium). Compared to CK, the N, NP, NK, and NPK application significantly increased τc by 49.6, 96.7, 73.6, and 36.2 %, respectively. Whereas, kd increased significantly only in the NPK treatment group. The optimal partial least squares regression model showed that mean weight diameter (MWD) had the greatest positive influence on soil critical shear stress, followed by fulvic acid (FA) content, whereas water-dissolved substances had a negative influence. Long-term balanced fertilizer application can increase MWD and τc by combining micro-aggregates and humus into large aggregates. Ca2+ content had the greatest positive effect on kd. Compared with that of CK, exchangeable Ca2+ content increased significantly with NP and NPK application (7.9 and 34.3 %, respectively). Ca2+ can increase kd by binding to the polar functional groups in FA to promote the shedding of hydration shells in large aggregates. Among all treatments, the NP treatment showed the best performance for reducing kd and increasing τc. This study could contribute to the understanding of the rill erosion process and modeling in non-calcareous soils and offer a reference for agricultural erosion control treatments.