Most of the studies reporting on nitrogen (N) loss from purple soil in the Three Gorges Reservoir region in China have focused only on soil losses and surface slope hydrological processes. Few investigations have addressed the fact that the N losses are associated with the dominant runoff process, and in particular with subsurface flow pathways. A simulation study was conducted in an area of purple soil near the Three Gorges Reservoir to evaluate the N losses associated with surface runoff and subsurface runoff under artificial rainfall simulation. Three rainfall intensities (low [0.5 mm min −1], moderate [1.0 mm min −1] and high [2.0 mm min −1]) and two fertilizer treatments (control [no fertilizer input] and fertilized [200 kg N hm −1]) were tested. The results showed that only subsurface flow was observed following the low intensity rainfall events. During moderate and high rain intensities, both surface flow and subsurface flow were observed. A prolonged low intensity rainfall is much more likely to cause subsurface flow and lead to larger volumes of subsurface runoff than a short high intensity rainfall. Generation of subsurface flow by means of macropores resulted in large N losses, especially of nitrate N (NO 3–N) which was mainly transferred by the subsurface flow, rather than the surface flow, during all rainfall events. In the control treatment, the average NO 3–N concentration in the subsurface flow was six times greater than that in the surface flow. In the 200 kg hm −1 N input treatment, the average NO 3–N concentrations in the subsurface flow from plots 1 and 2 were 23.83 and 25.62 mg l −1, respectively, which were more than twenty times as much as that in the surface flow. The fertilizer treatment greatly increased the loss of NO 3–N by subsurface flow. The average NO 3–N concentrations in the subsurface flow from the fertilized plots were over five times greater than from the non-fertilized plot. Under low intensity rainfalls, N loss, especially in the form of NO 3–N, was higher than under the other two rain intensities as a result of macropore flow. Up to a half of the total NO 3–N load was attributed to subsurface runoff from almost all the rainfall events (except for high intensity rainfall in plot 3). However, the application of urea fertilizer tended to have little effect on NO 3–N losses in the surface flow. Rainfall events after urea application probably enhanced NH 3–N loss in the surface hydrological pathway. In the purple soil region, the N loss is primarily governed by hydrological processes especially the subsurface flow, and local agricultural practices.