Fertilization plays an important role in soil nutrient loss from sloping croplands. However, the effect of fertilization on Molybdenum (Mo) loss remains unknown. The aims of this study were to explore the effects of different fertilizers of purple soil on the characteristics of soil molybdenum loss in surface, subsurface runoff and sediments. Five fertilizers treatments (3 replicates) were designed as following: no fertilizer (CK); conventional nitrogen, phosphorus, and potassium fertilizer (NPK); organic fertilizers with livestock manure (OM); nitrogen, phosphorus, and potassium fertilizer plus organic fertilizers with livestock manure (OMNPK); and straw turnover plus nitrogen, phosphorus, and potassium fertilizer (RSDNPK). The changes of runoff-related Molybdenum loss from June to September 2025 were studied. Results showed that fertilization significantly reduced surface runoff and sediment yield compared with CK (p < 0.05). The RSDNPK treatment exhibited the lowest surface runoff, while OM and OMNPK treatments most effectively decreased sediment loss. Dissolved Mo (DMo) was the predominant form of Mo loss across all treatments (50 similar to 70% of total loss), significantly higher than particulate Mo (PMo, 25 similar to 40%) and Mo of soil sediments (SEMo, 6.5 similar to 12.9%). Notably, the OM treatment uniquely shifted Mo loss toward subsurface flow (47.2% of total), whereas other treatments were dominated by surface runoff. Total Mo loss amount varied significantly among treatments (p < 0.05): CK (795 mu g/m(2)) > OM (685 mu g/m(2)) > NPK (596 mu g/m(2)) > OMNPK (533 mu g/m(2)) > RSDNPK (373 mu g/m(2)). The RSDNPK treatment achieved the optimal performance, reducing total Mo loss by 53.1% compared with CK. Structural equation modeling revealed that soil organic matter indirectly controlled Mo loss by modifying soil physical properties and hydrological processes. The findings demonstrate that RSDNPK represents the most effective strategy for minimizing Mo loss in purple soil sloping croplands, outperforming sole organic manure application. This study highlights the importance of organic amendment and management in Mo loss control and provides a scientific basis for sustainable nutrient management in erosion-prone agricultural systems.