Soil loss due to crop harvesting (SLCH) is a soil erosion process that signiifcantly contributes to soil degradation in crop-lands. However, little is known about soil nutrient losses caused by SLCH and its environmental impacts. In the North China Plain area, we measured the losses of soil organic carbon (SOC) and nitrogen as wel as phosphorus due to SLCH and assessed their relationship with soil particle size composition, agronomic practices and soil moisture content. Our results show that the losses by harvesting potato of SOC, total nitrogen (TN), available nitrogen (AN), available phosphorus (AP) and total phosphorus (TP) were 1.7, 1.8, 1.8, 15.9 and 14.1 times compared by harvesting sweet potato, respectively. The variation of SOC, N and P loss by SLCH are mainly explained by the variation of plant density (PD) (17–50%), net mass of an individual tuber (Mcrop/p) (16–74%), soil clay content (34–70%) and water content (19–46%). Taking into account the current sewage treatment system and the ratio of the nutrients adhering to the tubers during transportation from the ifeld (NTRP/SP), the loss of TN and TP by harvesting of potato and sweet potato in the North China Plain area amounts to 3% N and 20% P loads in the water bodies of this region. The fate of the exported N and P in the sewage treatment system ultimately controls the contribution of N and P to the polution of lakes and rivers. Our results suggest that a large amount of SLCH-induced soil nutrient export during transportation from the ifeld is a potential polutant source for agricultural water for vast planting areas of tuber crops in China, and should not be overlooked.