Smallholder farming systems make a vital contribution to food security. However, pests pose a significant challenge to the productivity and sustainability of these agricultural systems. The need to reduce the usage of chemical pesticides in agriculture has intensified due to growing public health and environmental concerns. Retaining generalized predators to biologically control pests is commonly considered as an alternative management strategy. Bats are widely acknowledged as highly effective pest suppression agents. However, little is known about how bats contribute to pest suppression services in smallholder farming systems and how different sympatric bat species divide their use of food resources. We employed DNA metabarcoding to determine the differential prey species consumed by seven bat species in Chinese smallholder farming systems to clarify pest suppression services and dietary niche differentiation. We detected 19 orders of arthropods, among which mosquitos (Diptera), moths (Lepidoptera), and beetles (Coleoptera) were the most predominant prey items. We also documented 75 major pests consumed by bats that can potentially damage agricultural areas or spread diseases. Moreover, there was a significant differentiation among the seven sympatric bat species. Finally, Spearman correlation analysis shows that morphological and echolocation traits may explain dietary niche differentiation. Our results suggest that bats play a critical role in pest suppression services in smallholder farming systems and further prove that the dietary niche was significant differentiation among bat species. These results implied that landscape heterogeneity in smallholder farming systems may increase arthropod diversity, in turn increase biological pest control by bats. Thus, our results also highlight the importance of conserving bat populations and their crucial ecosystem services in integrated pest management (IPM), which has significant implications for the potential protection of food security and human health.