High-value timber species such as monarch birch (Betula maximowicziana Regel), castor aralia (Kalopanax septemlobus (Thunb.) Koidz), and Japanese oak (Quercus crispula Blume) play important ecological and economic roles in forest management in the cool temperate mixed forests in northern Japan. The accurate measurement of their tree height is necessary for both practical management and scientific reasons such as estimation of biomass and site index. In this study, we investigated the similarity of individual tree heights derived from conventional field survey, digital aerial photographs derived from unmanned aerial vehicle (UAV-DAP) data and light detection and ranging (LiDAR) data. We aimed to assess the applicability of UAV-DAP in obtaining individual tree height information for large-sized high-value broadleaf species. The spatial position, tree height, and diameter at breast height (DBH) were measured in the field for 178 trees of high-value broadleaf species. In addition, we manually derived individual tree height information from UAV-DAP and LiDAR data with the aid of spatial position data and high resolution orthophotographs. Tree heights from three different sources were cross-compared statistically through paired sample t-test, correlation coefficient, and height-diameter model. We found that UAV-DAP derived tree heights were highly correlated with LiDAR tree height and field measured tree height. The performance of individual tree height measurement using traditional field survey is likely to be influenced by individual species. Overall mean height difference between LiDAR and UAV-DAP derived tree height indicates that UAV-DAP could underestimate individual tree height for target high-value timber species. The height-diameter models revealed that tree height derived from LiDAR and UAV-DAP could be better explained by DBH with lower prediction errors than field measured tree height. We confirmed the applicability of UAV-DAP data for obtaining the individual tree height of large-size high-value broadleaf species with comparable accuracy to LiDAR and field survey. The result of this study will be useful for the species-specific forest management of economically high-value timber species.