The invention discloses a method for measuring a canopy gap three-dimensional structure based on laser radar. The method includes a first step of obtaining and pre-treating laser radar data which is remote sensing data obtained by laser radar loaded on a fixed wing aircraft or an unmanned aerial vehicle, the data of each laser point including X, Y, Z coordinate data and echo intensity data, a second step of processing canopy layer data, a third step of identifying canopy gaps, and a fourth step of measuring a three-dimensional canopy gap structure. The method is easy to realize, and is not affected by surveyed land and forest types and ground situations. Rapid, accurate, large-scale and multi-dimensional canopy structure measurement can be realized.