Serious point source and non-point source pollution in Xiaoqinghe River Basin, primarily caused by advanced industries and agriculture, have resulted in the excess of river water total nitrogen, which further have deteriorated the aquatic ecology and environment of Xiaoqinghe Estuary and Laizhou Bay. Based on observed streamflow and total nitrogen data, the SWAT model, established for Xiaoqinghe River Basin, has been calibrated and verified. Then, the spatial and temporal characteristics of total nitrogen load for the period of 2008-2013 have been simulated and analyzed, and the pollution source of total nitrogen has been identified. The results show that accordant with the annual streamflow, the annual total nitrogen load indicates an obvious inter-annual variability with the annual average value of 38.0×103 t. Spatially, total nitrogen load is relatively high for various sub-basins, among which the highest output in the sub-basins located in Shouguang City and Zhangqiu City with advanced agriculture, Zouping County with many engineering enterprises, Jinan urban district with high population density. The primary source of total nitrogen load is dominated by non-point pollution source. Nitrogen losses from agriculture fertilizer and livestock manure account for 32.5% and 29.5%, respectively of the total nitrogen load. In addition, nitrogen emissions from industries and urban wastewater contribute greatly to the total nitrogen load with the proportion of 19.4% and 16.5%, respectively. Therefore, point and non-point pollution source should be overall considered for the total amount control and reduction of total nitrogen in Xiaoqinghe River Basin.