Plant–frugivore networks often display vertical structure in forest communities because of vertical distribution of fruit resources and animal feeding niches on and under trees. However, how vertical stratification of fruit sources and animal feeding niches affect the structure and functioning of frugivory networks has not previously been well studied. We used infrared cameras under trees and direct observations on trees to extensively sample the whole frugivory networks in a subtropical forest in Southwest China. We analyzed the structure of on‐the‐tree, under‐the‐tree, space‐free aggregated (where links lacked vertical spatial information), and space‐based aggregated frugivory networks (where links included vertical spatial information). We uncovered vertical differentiation in frugivore composition (dissimilarity > 0.7) and less than 5% overlap of links occurring both under and on trees. Network analyses revealed high complementarity between the under‐ and on‐the‐tree frugivory networks. Modularity and specialization increased when space‐based hidden links (i.e. considering spatial locations) were included. Overall, we conclude that consideration of vertical structure (on‐the‐tree versus under‐the‐tree) in frugivore networks can enhance our understanding of the seed dispersal process and frugivore co‐existence in forests.