Nitrogen is the main driving factor for the eutrophication of Lake Erhai. Thus, it is significant to clarify the spatial and temporal distribution characteristics of nitrogen in rural and urban areas of the watershed. In this paper, an output coefficient model was applied to quantify nitrogen pollution loading and identify the main sources of nitrogen from urban and rural area during 1998-2016. With the help of spatial analysis function of GIS, the river export of nitrogen to Lake Erhai from sub-basins was quantified. The results showed that the total nitrogen (TN) pollution loading in 1998, 2005, 2010 and 2016 was 2442.43, 2573.10, 2606.28 and 2389.10 t, respectively. Point pollution was increasing while non-point source pollution showed a downward trend over time, whereas non-point pollution was still the main source of TN. From the perspective of sources retrieval, the fertilizer input, livestock and poultry breeding and rural population were the main sources in the Lake Erhai basin, accounting for 35%, 24% and 17% of the TN loading, respectively. In 2016, the load per unit area was mainly on 1000-1500 kg/km², with higher loads in the Zhonghexi (1857 kg/km²), Taomeixi (1582 kg/km²), Baishixi (1541 kg/km²), Luoshijiang (1088 kg/km²) and Boluojiang (1050 kg/km²) sub-basins. In order to reduce the nitrogen losses to the water bodies and mitigate eutrophication status of Lake Erhai, several actions could be favorably suggested in the future:the sewage treatment rate could be improved through building more centralized treatments of domestic sewage; animal manure treatment technology could be improved to increase the nitrogen use efficiency in the animal production process; and finally, synthetic fertilizer and animal manure could be used more rationally.