Agricultural intensification through increasing fertilization input and cropland expansion has caused rapid loss of semi-natural habitats and the subsequent loss of natural enemies of agricultural pests. It is however extremely difficult to disentangle the effects of agricultural intensification on arthropod communities at multiple spatial scales. Based on a two-year study of seventeen 1500 m-radius sites, we analyzed the relative importance of nitrogen input and cropland expansion on cereal aphids and their natural enemies. Both the input of nitrogen fertilizer and cropland expansion benefited cereal aphids more than primary parasitoids and leaf-dwelling predators, while suppressing ground-dwelling predators, leading to an disturbance of the interspecific relationship. The responses of natural enemies to cropland expansion were asymmetric and species-specific, with an increase of primary parasitism but a decline of predator/pest ratio with the increasing nitrogen input. As such, agricultural intensification (increasing nitrogen fertilizer and cropland expansion) can destabilize the interspecific relationship and lead to biodiversity loss. To this end, sustainable pest management needs to balance the benefit and cost of agricultural intensification and restore biocontrol service through proliferating the role of natural enemies at multiple scales.