The hydrological processes of red soil slope farmland are complex, and the vertical migration of nitrogen (N) is influenced by these processes, which present different layering characteristics of water flow. Previous studies on the vertically stratified transport of N on slope soils have mainly relied on rainfall simulation, lacking a comprehensive study of the overall process of N leaching from surface soil to underground under natural conditions. To investigate the impact of these hydrological processes on the transport of N at different layers under natural rainfall events, large-scale field runoff plots were constructed as draining lysimeters to conduct a consecutive 2-year observation experiment at Jiangxi Soil and Water Conservation Ecological Science and Technology Experimental Station, China. The runoff (the water of 0 cm), interflow, deep percolation, soil moisture content (SMC), total nitrogen (TN), nitrate nitrogen (NO3--N) and ammonium nitrogen (NH4+-N) concentrations were monitored and determined. The N loss of red soil farmland under two treatments, namely grass mulching (FC, a coverage of 100% with Bahia grass) and exposed treatment (BL, without anything covered), were measured. The relationships between hydrological factors and different forms of N losses were analyzed. The results indicate the following: (1) Deep percolation is the main pathway of water loss and N loss for red soil slope farmland, accounting for over 85% of the total water loss and N Loss. Grass mulching can significantly reduce surface runoff and N loss. (2) Vertically stratified N is mainly NO3--N, and the concentrations of each form of N show the same trend: deep percolation > interflow > runoff. (3) Water loss, rainfall, and SMC are closely related to the stratified loss of N, with correlation coefficients ranging from 0.74 to 0.98. The correlation analysis and redundancy analysis (RDA) on the relationships between different forms of N losses and hydrological factors indicate that rainfall was the primary factor driving the stratified loss of N in red soil slope farmland.