Nine gemstone samples were analysed by using a portable X-ray fluorescence-X-ray diffraction (XRF-XRD) system without any destructive preparation processes. The samples were measured by groups based on the transparency and the complexity of molecular structure. The XRF and the XRD measurements for each sample were performed simultaneously.The key experimental parameters were optimized in order to obtain XRD patterns acceptable for phase identification in a limited time. The XRF spectrum of each sample was analysed first to acquire the elemental composition qualitatively, and the information was then applied to refining possible phases. The phase analysis process of each sample was described in detail and the most likely phases were determined. Normal XRD experiments were conducted in order to verify the results. Advantages, disadvantages and applicable range of the system were analysed. The results indicate that the portable XRF-XRD system can be applied to identifying particular gemstones effectively, while single-crystal gems may not be identified very well. Wider recognition and application of the portable XRF-XRD system in cultural heritage and gemological fields call for hardware development, software updating and more real application cases.