The disclosure provides a structure diagnosis system and a structure diagnosis method. The structure diagnosis system includes: a lidar scanner scanning a structure to generate a point cloud data; an input interface receiving the point cloud data; and a processor receiving the point cloud data and generating a point cloud data set. The processor executes a surface degradation and geometry abnormal coupling diagnosis module to: marking a first point cloud range of a surface degradation area according to color space value of the point cloud data set; marking a second point cloud range of a geometry abnormal area according to coordinate value of the point cloud data set; when an abnormal area includes the first point cloud range and the second point cloud range at least partially overlapping each other, determining surface degradation or geometry abnormal occurring at the abnormal area and mark the abnormal area with a predetermined mode.