An on-line photochemical vapor generation (PCVG) method for highly sensitive speciation analysis of selenium was proposed by using metal organic framework (MOF) MIL-125-NH2 as a catalyst. When it was coupled with HPLC (high performance liquid chromatography)-ICPMS (inductively coupled plasma mass spectrometry) for Se separation and detection, inorganic selenium species (Se(IV) and Se(VI)) were firstly separated in HPLC with Na2CO3-NaHCO3 as an eluent, and then mixed with MIL-125-NH2 nanoparticles and formic acid in the PCVG reactor to form gaseous selenium-containing species under ultraviolet irradiation, which was introduced into ICPMS for selenium measurement after gas–liquid separation from the reaction solution. Experimental factors of HPLC separation, PCVG reaction and ICPMS detection were carefully investigated. Under the optimized conditions, the limits of detection (LOD) for Se(IV) and Se(VI) were found to be both as low as 0.8 ng/mL. The relative standard deviation (RSD) of Se(IV) and Se(VI) were 4.6% and 3.7% at 20 ng/mL (n = 11), respectively. Certified reference materials and bottled natural mineral water samples were successfully analyzed by the proposed method.