Agricultural nonpoint source (NPS) pollution is still the main factor that affects the quality of rivers, lakes, and reservoirs. Starting from the study of the mechanism of NPS, taking the Yangliu small watershed in the Shaanxi section of the Hanjiang River Basin in China as an example, and based on the combination of measured data and models, this paper focused on the analysis of the characteristics of NPS between the runoff plot and small watershed. The results showed that with the rainfall and surface runoff, the nutrient concentration increased first and then decreased, and the highest occurred in the first half of the whole rainfall process. Rainfall, maximum rainfall intensity at 60 min (I60), runoff, and suspended sediment (SS) were all related to nutrient diversion loss. However, the correlation among rainfall, I60, and runoff and the content of various forms of nitrogen and phosphorus were significantly higher than that of SS. Crop interplanting and terrace planting could play a significant role in reducing sediment and nutrient loss. For the analysis of NPS pollution in small watersheds, the time-variant gain model (TVGM) was used to simulate the missing flow in some months of the basin during the flood season. The average concentration method was used to calculate the NPS pollution load in flood season. It was found that total nitrogen (TN) and total phosphorus (TP) accounted for more than 92% and 69%, respectively. This study is expected to provide scientific basis for NPS pollution control in areas both regionally and worldwide.