Trabecular microstructure is an important factor in determining bone strength and physiological function. Normal X-ray and computed tomography (CT) cannot accurately reflect the microstructure of trabecular bone. High-resolution peripheral quantitative computed tomography (HR-pQCT) is a new imaging technique in recent years. It can qualitatively and quantitatively measure the three-dimensional microstructure and volume bone mineral density of trabecular bone in vivo. It has high precision and relative low dose of radiation. This new imaging tool is helpful for us to understand the trabecular microstructure more deeply. The finite element analysis of HR-pQCT data can be used to predict the bone strength accurately. We can assess the risk of osteoporosis and fracture with three-dimensional reconstructed images and trabecular microstructure parameters. In this review, we summarize the technical flow, data parameters and clinical application of HR-pQCT in order to provide some reference for the popularization and extensive application of HR-pQCT.