The confocal micro X-ray fluorescence technology based on two polycapillary X-ray lenses is used to analyze the elements in the medicines with capsule non-destructively. In this technology, two confocal lenses form confocal volume, and only the X-rays from the confocal volume can be detected by the detector, which ensures non-destructive and in-situ analysis of elements in the capsule shell and the medicine inside to identify their species. X-ray fluorescence spectral characteristics of four types of medicines with capsule are analyzed. The experimental results show that different medicines have different X-ray fluorescence spectra, and different spectra correspond to different elemental compositions, which could be used to identify medicines. The confocal micro X-ray fluorescence technology can be used in the non-destructive and in-situ analysis of the samples with capsule, and has potential applications in identifying the types and the authenticity of medicines with capsule.