The effect of dicarboxylic acids with a three C-C bonds distance on the crystallization of calcium oxalate (CaOxa) was investigated in silica gel system by means of X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). These acids include succinic acid, maleic acid, fumaric acid, malic acid, L-aspartic acid and tartaric acid. All the dicarboxylic acids can inhibit the aggregation of calcium oxalate monohydrate (COM) and induce the formation of calcium oxalate dehydrate (COD). But their ability to inhibit the growth and aggregation of COM, to diminish the specific surface area of COM and to induce COD formation were strengthened as the number of the substituted hydroxyl or amino group increased. The molecular mechanisms were discussed in terms of chemical structures of dicarboxylic acids. Only the dicarboxylic acids with a HOOC-CH(R)-CH2-COOH (R=OH or NH2) group were found to have the best inhibitory effect on the CaOxa urinary stones. The results could provide some clue to looking for new drugs for urinary stones in clinic.