The concentration and sources of organic nitrogen (ON) in lake sediment significantly affect the lake nitrogen cycle. However, the influencing factors and contributors to the ON accumulation rate (ONAR) are unclear. In this study, tree sediment cores from northern, eastern, and southern Dianchi Lake (DC-N, DC-E, and DC-S, respectively), sampled in July 2014, were used to study the effects of autochthonous and allochthonous sources on ON. The results showed that ON and the ONAR increased 2.4–5.1 and 2.6–4.8 times, respectively, from1900 to2000, especially since the 1980s, at which point algal blooms occurred more frequently. The ON contents decreased in the order: DC-S > DC-N > DC-E, whereas the ONAR values followed the order: DC-N > DC-S > DC-E, suggesting that the ONAR was influenced by ON content as well as depositional environmental conditions. The total concentrations of n-alkanes (n-C12 to n-C34) ranged from 4719.4 ng g− 1 to 61,959.6 ng g− 1 in the three sediment cores, each of which exhibited different n-alkanes characteristic variation with vertical depth. The sources of ON were mainly allochthonous (soil erosion and terrestrial plants) and autochthonous (algal and aquatic plants) in DC-S and DC-N, respectively, whereas they were primarily mixed planktonic and terrestrial sources in DC-E. Using the stochastic impacts by regression on population, affluence, and technology model to further examine the ONAR values revealed that 1% increase in temperature and nitrogen fertilizer can increase the ONAR by 73.8–86.2% and 73.2–151.3% in all sediments, especially in DC-S and DC-E. However, a 1% increase in construction area could reduce the ONAR by 2.4–14.2%, especially in DC-N. Overall, climate change and human activities determine the spatial and temporal ONAR variation in Dianchi Lake.