In this study, we investigated net primary production (NPP) and nutrient cycling in an apple orchard-annual crop system located in the Hill and Gully Region of the Loess Plateau, which included four production subsystems: Qinguan apple, Fuji apple, corn and millet. The results showed that NPP of corn (Zea mays L.) was two to three times greater than for millet (Setaria Italica L.) or apples (Malus domestica Borkh., cv Fuji' and Qinguan'). Annual nutrient uptake by corn and millet was also much larger compared to apple trees. A comparison of nutrient use efficiency based on economic product showed that P and K use efficiency for Qinguan apples was about 50% greater compared to corn, while there was little difference in N use efficiency between apples and corn. More than 94% of the nutrients taken up by annual crops were lost from the system through the removal of grain and above-ground crop residue. In contrast, apple harvest and tree pruning resulted in the removal of 10-50% of the nutrients taken up annually by apple trees. Calculations indicated that farmers applied 60 times more N and 33 times more P to Qinguan apple orchards than was removed by apple harvest, but the amount of N and P fertilizer applied to corn was slightly less than the amount of N and P removed through crop harvest. In summary, the results indicated that increasing the proportion of land planted to apples and convincing farmers to leave annual crop residue in the fields would increase the sustainability of the apple orchard-annual crop system. Additional work needs to be done to determine the fate of N and P fertilizer applied to orchards as well as optimum fertilization rates for each of the four crops in the apple orchard-annual crop system.