Excessive fertilizer application, majorly nitrogen- and phosphorus-based fertilizers, in farmland has intensified environmental pollution of rivers, lakes, and other surface water bodies worldwide by agricultural non-point sources, especially the highly-mobile nitrogen. To solve nitrogen pollution in sugarcane areas, exploring the nitrogen output characteristics of agricultural watersheds in crop fields becomes necessary. Therefore, the objective of the study was to evaluate the characteristics of nitrogen output during typical rainfall events in different sugarcane growth stages in a southern tropical watershed in China. Dynamic monitoring of runoff and nitrogen concentration was carried out for four rainfall events and compared among four sugarcane growth stages (Establishment; Vegetative growth; Grand growth; Ripening) during the growing season of 2018 in the Nala watershed, Kelan Reservoir, Guangxi, China. The results showed that the total dissolved nitrogen flux of the 4 rainfall events ranged from 0.08 to 9.88 kg·hm−2 for the different growth stages. Nitrate nitrogen was the main component of the total flux, accounting between 75.7 and 92.1% of the total dissolved nitrogen while ammonium nitrogen accounted between 1.80 and 5.26% of the total flux for the 4 rainfall events. Total dissolved nitrogen and nitrate-nitrogen were significantly and negatively correlated with runoff (p < 0.05), while total dissolved nitrogen concentration did not correlate with runoff. The incipient scouring effect of total dissolved nitrogen and nitrate-nitrogen was not noticeable. The concentration of total dissolved nitrogen in the Nala watershed was inferior to class V water quality standard, indicating water eutrophication danger. The study showed that nitrogen nutrient inflow into the river was promoted by N-fertilization time and rainfall. Therefore, reasonably reducing N-fertilization dose and post-rain fertilization could effectively reduce nitrogen inflow into rivers and avoid the intensification of eutrophication in sugarcane areas. We recommend multiple years of studies to verify the possible impacts of differences in weather conditions.