Accurately converting nonpoint source pollution loads from the watershed scale to administrative scale is challenging. A promising solution is calculating the pass-through rate coefficient of nonpoint source pollutants (PTRE–NPS) at the watershed scale and discretizing the watershed units on grids with the same area but with different PTRE–NPS information. However, the pollution load of agricultural nonpoint sources has received far more attention than the PTRE–NPS. Moreover, as most of the existing PTRE–NPS results are obtained by distributed, semi-distributed models and the field monitoring of small watersheds, they are not easily extended to the national-scale management of nonpoint source pollution. The present study proposes a new conception of PTRE-NPS and tests it on different spatial scales by a coupled model, which captures the entry of agricultural nonpoint source pollutants into rivers and lakes. The framework includes five major modules: a pollutant driving and loss module, a surface runoff module, a soil erosion module, a subsurface runoff module, and a retention module. The model was applied in simulations of agricultural nonpoint source pollution in the Hongfenghu reservoir watershed with a karst hydro-geomorphology, which exists in the mountainous region of southwest China. On the watershed scale, the PTRE–NPS of total nitrogen (TN) and total phosphorous (TP) ranged from 0 to 2.62 (average = 0.18) and from 0 to 3.44 (average = 0.19), respectively. On the administrative scale, the PTRE–NPS of TN and TP were highest in Baiyun Town. The TN and TP loads of the agricultural nonpoint source pollution in the rivers and lakes of the Hongfenghu reservoir watershed were 1707.78 and 209.03 t, respectively, with relative errors of −45.36% and 13.07%, respectively. Most importantly, the developed framework can scientifically represent the generation–migration–transmission process of agricultural nonpoint source pollutions in each grid at both the watershed and administrative scales.