Visual adaptation produces remarkable perceptual aftereffects. However, it remains unclear what basic neural mechanisms underlie visual adaptation and how these adaptation-induced neural changes are related to perceptual aftereffects. To address these questions, we examined transparent motion adaptation and traced the effects of adaptation through the motion processing hierarchy. We found that, after adapting to a bidirectional transparent motion display, observers perceived two radically different motion aftereffects (MAEs): segregated and integrated MAEs, depending on testing locations. The segregated MAE yielded an aftereffect opposite to one of the adapting directions in the transparent motion stimulus. Our results revealed that the segregated MAE relies on the integration of local adaptation effects. In contrast, the integrated MAE yielded an aftereffect opposite to the average of the adapting directions. We found that integrated MAE was dominant at non-adapted locations but was reduced when local adaptation effects were weakened. These results suggest that integrated MAE is elicited by a combination of two mechanisms: adaptation-induced changes at a high-level processing stage and integration of local adaptation effects. We conclude that distinct perceptual aftereffects can be observed due to adaptation-induced neural changes at different processing levels, supporting the general hypothesis of multilevel adaptation in the visual hierarchy.