In situ non-destructive imaging of characteristic microstructures of wild ginseng are investigated by synchrotron radiation X-ray propagation-based phase-contrast computed tomography (PPCT), and phase-attenuation duality Paganin algorithm (PAD-PA), a phase retrieval algorithm, is employed to process the experimental PPCT data, and the three-dimensional imaging of wild ginseng, such as the quantitative volume, the region and number distributions of calcium oxalate are obtained. The results show that PPCT combines with PAD-PA phase retrieval algorithm is well suit for quantitative study and analysis of microstructures of traditional Chinese medicines like wild ginseng.