<p>Intercropping is an agricultural practice applied worldwide to promote biodiversity and biological control services in an agroecosystem. Here, we assessed the differences in arthropod communities in the canopy between pecan (<i>Carya illinoinensis</i>) orchards intercropped with two flowering crops, rapeseed (<i>Brassica rapa</i>) and sunflower (<i>Helianthus annuus</i>), and monoculture pecan orchards. Our results showed that introducing rapeseed and sunflower changed the community composition of arthropods in the canopy. Compared with the monocropping system, the abundance of total arthropods and arthropod herbivores in the intercropping system was reduced, while the abundance of arthropod natural enemies and neutral arthropods significantly increased. The richness and Shannon diversity index of total arthropods and arthropod natural enemies, as well as the Shannon diversity index of arthropod herbivores, were dramatically higher in the intercropping system. However, the effect of the cropping system on the Shannon diversity index of neutral arthropods showed annual variation. Furthermore, compared to the monocropping system, the intercropping system displayed a more complex co-occurrence network structure and stronger co-occurrence patterns among arthropod natural enemies, arthropod herbivores, and neutral arthropods. Our study indicated that intercropping with rapeseed and sunflower can significantly improve arthropod communities in the canopy in pecan orchards and enhance biological control potential.</p>