The invention relates to a double splitflow nano upgrade liquid phase chromatogram online desalting, enrichment and mass spectrum combination system which comprises a pump, a first splitter, a second splitter, a sample valve, a switching valve, a backpressure valve, a capillary tube separation column and a mass spectrometer, wherein, the pump, the first splitter, the sample valve, the second splitter, the capillary tube separation column and the mass spectrometer are connected in series in turn through pipelines; the split ports of the first splitter and the second splitter are respectively connected with the two inlets of the switching valve through the pipelines; moreover, the outlet of the switching valve is connected in series with the backpressure valve and then is communicated with a waste fluid pool through the pipeline. The system has the advantages that: during the sampling and separation of sample, the system has less pressure fluctuation; with small pre-column dead volume, the system overcomes the gradient delay effect caused by large-volume sampling adopted in the prior nano upgrade liquid phase separation system; with excellent separation repeatability, the system is particularly suitable for gradient separation; meanwhile, the system can be used in online desalting, enrichment and mass spectrum combination of sample with high salinity and low concentration; moreover, the system has a simple structure, convenient operation and easily realized automation.