Abstract: The accurate mass determination method of fluorescent dye-labeled oligonucleotides by high resolution inductively coupled plasma mass spectrometry (HR-ICP-MS) was established. This method allows for the mass of fluorescent dye-labeled oligonucleotides to be traceable to the SI. The fluorescent dye-labeled oligonucleotides was processed by column chromatography、ultracentrifugation、dialysis。The purity was detected by electrophoresis chip and electrical conductivity。The fluorescent dye-labeled oligonucleotides was digested with microwave in nitric acid. The phosphorus from the fluorescent dye-labeled oligonucleotides was quantitative determined by the HR-ICP-MS. The parameters of HR-ICP-MS and microwave digestion was optimized. The interference factors of HR-ICP-MS such as physical interference, signal drift interference, isotopes, phosphorus element speciation interference was analyzed and corrected with ultra-filtration, internal standard of Y（88.906）, certified reference material of phosphate, nucleotide, oligo DNA. The uncertainty in measurement was evaluated mainly from method precision, Phosphorus CRM, Nitric acid digestion, Weight of sample and CRM. A uncertainty (< or = 8.28%) was smaller than ultraviolet spectrophotometry, fluorescence spectrophotometry and real time PCR. This method will aide in the development of Certified Reference Materials (CRMs) with certified nucleic acid（DNA、RNA） content.