Overland flow is one of the important factors inducing soil nutrients loss into runoff. In order to simulate and study the effects of overland flow on soil nutrients loss, a mathematical model describing soil nutrients transport with overland flow was developed based on the concept of effective mixing depth and Kostiakvo equation. In addition, the model also makes the corresponding assumptions to simplify the infiltration process. The obtained model was denoted as the incompletemixing model. Field water scouring experimental data was adopted to test the applicability of the proposed model. The experiment was performed on a natural, fallowed loessial slope (38°46′~38°51′N, 110°21′~110°23′E), in 14km west of the Shenmu Erosion and Environment Research Station of the Institute of Soil and Water Conservation, Chinese Academy of Sciences, in the Liudaogou watershed, Shaanxi Province. Field plots were established on a slope that had been fallowed for seven years. Vegetation types cover were adopted (herbaceous and crops), including caragana and soybean. The characteristics of the transport of runoff, nutrients (nitrogen and phosphorus) under different vegetation cover were discussed in this study. Results indicated that the incompletemixing model performed pretty well in predicting the process of nutrients transport into runoff. The correlation coefficients were larger than 0.9 for all the treatments. Moreover, little bias was observed between the measured cumulative mass and the simulated data obtained from the incompletemixing model. Taking nitrate nitrogen for example, the relative errors between the measured data and simulated results were 6.6% (caragana) and 5.9% (soybean). When the nutrient was soluble phosphorus, the relative errors were 1.1% (caragana) and 2.3% (soybean). For better simulation results, the calculation accuracy and simplicity in obtaining parameters should be taken into consideration during model selection. The results in this study will provide significant references for more analysis on nutrients transport into runoff with overland flow in future.