The handheld X-ray fluorescence spectrometer (XRF) has the advantages of being easy to carry, simple in operation, non-destructive, and offers fast and relatively accurate detection, while synchrotron radiation X-ray absorption spectroscopy (XAS) has been used for the selenium (Se) speciation of Se-enriched yeast and Se hyperaccumulators. In this study, we propose the application of a handheld XRF in combination with XAS for the fast quantification and speciation of Se in commercially available dietary supplements. The results of total Se determined by handheld XRF were in good agreement with ICP-MS data, which was also consistent with the labeled value of Se dietary supplements. The XAS analysis of the tested samples showed that Se was mainly present in the form of organic Se. The proposed method is practical and simple for high throughput label verification and quality control of Se dietary supplements. It can, therefore, be a useful method not only for researchers but also for regulators and producers in the analysis of Se dietary supplements.