Landscape fragmentation and defaunation have major impacts on plant dispersal and dynamics. However, whether the impact of such perturbations on seed dispersal and recruitment change in sign and strength across habitats and spatial scales, and whether they amplify or buffer each other, remains largely unknown. To evaluate, for the first time, the joint impact of fragmentation and defaunation on seed dispersal effectiveness (SDE) across spatial scales (e.g., short‐ and long‐distance seed dispersal), we utilized the long‐term field data of a mammal‐dispersed tree (Pyrus bourgaeana) in a spatially explicit individual‐based model. By means of simulation experiments, we evaluated the effects of different levels of landscape fragmentation and defaunation on SDE and tree recruitment. Our simulation results revealed that the direction and magnitude of the fragmentation effect on SDE depended on its strength (mild, severe) and the spatial scale considered. Severe fragmentation decreased SDE for short‐ and intermediate‐distance seed dispersal. Interestingly, mild and severe fragmentation increased SDE of long‐distance seed dispersal, suggesting a positive effect of such perturbations (i.e., an increase in the proportion of successful long‐distance dispersal events). Though defaunation had a consistently negative effect on overall SDE, its magnitude was highly species‐ and spatial–scale‐dependent. The impact of defaunation on seed dispersal distance was also species‐specific: the proportion of long‐distance dispersal increased under total badger (Meles meles) defaunation but decreased under total fox (Vulpes vulpes) defaunation. A pervasive integration of seed dispersal distance into the SDE framework is essential to most comprehensively understand the scale‐dependent nature of human activity impacts on plant dynamics. In the long term, strong perturbations (landscape fragmentation and defaunation) could select either for or against long‐distance seed dispersal, altering in different ways the ability of plants to cope with climate change.