Abstract: Small molecules, including arginine, mannitol and dipeptide were analyzed by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) using a low concentration of isoliquirigenin (ISL, 0.05 mmol/L) as a matrix. In comparison with 2,5-dihydroxybenzoic acid (DHB) and 2,4,6-trihydroxyacetophenone (THAP), ISL exhibited outstanding matrix properties as follows: 1) higher homogeneity of crystallization thus allowing automatic data acquisition; 2) better spectral quality in terms of resolution and signal to noise ratio (S/N); 3) better salt tolerance. The study has an important role in organic compounds as matrix for analyzing small molecules, and can open up a new prospect.