In order to solve the problems of conventional pearl identification methods, which require the testing personnel to have rich experience, sample pretreatment, sample destruction and long detection time, a dual-mode pearl detection system based on X-ray transmission imaging and fluorescence was designed. X-ray attenuation coefficient could be calculated by the introduction of a thickness measurement system on X-ray transmission imaging system. The attenuation coefficient of the material can be calculated, which makes samples with the same X-ray absorption, different thickness and similar attenuation coefficient can be distinguished, and the resolution of the imaging system can be improved. The thresholds database of attenuation coefficients was established by measuring a large number of samples. By comparing the attenuation coefficient with the threshold value, the identification between different imitation pearls, pearls and imitation pearls could be realized. The content of Ca in freshwater and seawater pearls with similar attenuation coefficients is much larger than that of Sr, and the content of Sr in freshwater and seawater pearls is different. The ratio of contents of Sr and Ca be used to distinguish between freshwater and seawater pearls. Therefore, X-ray fluorescence analysis system is introduced. The fluorescence intensity ratios of Sr and Ca in fresh water and seawater pearls were measured, and the threshold value of the fluorescence intensity ratio between freshwater and seawater pearls was calculated by a large number of sample measurements, and the identification of freshwater and seawater pearls was performed based on the comparison between the measured values and the threshold values. The X-ray transmission imaging system and the X-ray fluorescence system introduced into the thickness measurement system cooperate to form a dual-mode system for identifying pearls. The experimental results show that the dual-mode system can distinguish between different imitation pearls, pearls and imitation pearls, freshwater and seawater pearls without destroying the sample. The dual-mode detection system can be used for online many-sample inspection in conjunction with the sorting system and has potential applications in such fields like the analysis identification of jewelry, ore, and lithoid flooring.