A simple and easy-to-build high-throughput analysis system was constructed. The system consisted of three major components: (1) a multichannel device with 16 parallel capillaries, (2) a desorption electrospray ionization (DESI) source, and (3) a linear ion trap mass spectrometer. When analyses were performed, the multichannel device was moved horizontally on a translation stage controlled by a step motor. Our design expands the functions of DESI, in which the liquid sample in capillary was driven out by the nebulizing gas, ionized, and then transferred to a mass spectrometer. To assess the high-throughput performance of the system, 5 mg/L 1,3-diethyl-1,3-diphenylurea (DDU) solution and 10 mg/L angiotensin I solution were alternatively loaded into the reservoirs and capillaries in the multichannel device. Results indicated that analyses of the all the samples in 16 capillaries were completed within 1.6 min, which means a throughput of 600 samples/h. Reactive DESI experiment was also successfully performed with this system to show the feasibility of online derivatization. The relative standard deviations for a single capillary and five identical capillaries were 7.6 (n = 16) and 12.3%, respectively. Linear relative abundance response was achieved for DDU (r = 0.9971).