The dataset contains top-of-canopy height before and after the 2015-15 El Niño Southern Oscillation (ENSO) event across a human-modified tropical landscape in Malaysian Borneo. The derived changes in top-of-canopy height from 36,655 repeated measurements were investigated. Data were obtained from airborne LiDAR in November 2014 and April 2016. Topographic Position Index and distance from oil palm plantations are also included to investigate the effects of topography and fragmentation on the canopy height change during the ENSO event. Each observation (pixel) contains the coordinates to assess the spatial effects on canopy changes.