Forest degradation through logging is pervasive throughout the world’s tropical forests, leading to changes in the three‐dimensional canopy structure that have profound consequences for wildlife, microclimate and ecosystem functioning. Quantifying these structural changes is fundamental to understanding the impact of degradation, but is challenging in dense, structurally complex forest canopies. We exploit discrete‐return airborne LiDAR surveys across a gradient of logging intensity in Sabah, Malaysian Borneo, and assess how selective logging has affected canopy structure (Plant Area Index, PAI, and its vertical distribution within the canopy). LiDAR products compared well to independent, analogue models of canopy structure produced from detailed ground‐based inventories undertaken in forest plots, demonstrating the potential for airborne LiDAR to quantify the structural impacts of forest degradation at landscape scale, even in some of the world’s tallest and most structurally complex tropical forests. PAI estimates across the plot network exhibited a strong linear relationship with stem basal area (R2 = 0.95). After at least 11‐14 years of recovery, PAI was ~28% lower in moderately logged plots and ~52% lower in heavily logged plots than in old‐growth forest plots. These reductions in PAI are associated with near‐complete lack of trees >30‐m tall, which has not been fully compensated for by increasing plant area lower in the canopy. This structural change drives a marked reduction in the diversity of canopy environments, with the deep, dark understory conditions characteristic of old‐growth forests far less prevalent in logged sites, with full canopy recovery likely to take decades. Synthesis and Applications. Effective management and restoration of tropical forests requires detailed monitoring of the forest and its environment. We demonstrate that airborne LiDAR can effectively map the canopy architecture of the complex tropical forests of Borneo, capturing the three‐dimensional impact of degradation on canopy structure at landscape scales, therefore facilitating efforts to restore and conserve these ecosystems.