The work shown here describes a simple, fast and effective on-line solid phase extraction (on-line SPE) method for facilitative high-throughput sample desalting before the detection of mass spectrometry(MS)or liquid chromatography-mass spectrometry(LC-MS). This method includes single SPE column mode and dual SPE column mode. It accomplishes the on-line desalting with an Ultimate 3000 HPLC system equipped with a dual pump system (loading pump/analytical pump), an autosampler, a column oven equipped with a 2p-10p valve, controlled by a chromatography data system. In the single SPE column mode, sample loading and desalting were performed on the SPE column using the loading pump. The analytes were retained on the SPE column, and the salt in the sample solution was flushed out of the SPE column. After desalting, the retained analytes were eluted from the SPE column with the analytical pump. In the dual SPE column mode, two same SPE columns were used. Firstly, the sample loading and desalting were performed on the SPE column 1. The analytes were retained and the salt was flushed out. After desalting on the SPE column 1, the sample loading and desalting were performed on the SPE column 2. Meanwhile, the retained analytes were eluted from the SPE column 1 with the analytical pump. As both of the processes on the SPE columns 1 and 2 described above completed, the sample loading and desalting on the SPE column 1, and the elution of the analytes from the SPE column 2 started again. As the SPE columns 1 and 2 worked in turn, the on-line SPE desalting system was efficient. The eluted analytes from the SPE columns may be determined by MS directly, or separated on the analytical column and then determined by MS/UV.