Twelve fully optimized geometries of uracil-H2O, uracil-H2S and uracil- H2Se complexes have been obtained with density function theory (DFT) method at the B3LYP/6-311++G** level. The intermolecular interaction energy is calculated with zero point energy (ZPE) correction and basis set superposition error (BSSE) correction. The greatest corrected intermolecular interaction of the uracil-water complexes is -31.503KJ/ mol, -12.750KJ/mol and -10.997KJ/mol, respectively, indicating that the intensity of interaction between uracil and H2O is stronger than that of uracil-H2S and uracil-H2Se. Natural bond orbital (NBO) analysis is performed to reveal the origin of the interaction. Frequency calculations are carried out on each optimized structure, and their IR spectra are discussed. Vibrational analysis show that there are large red-shifts for H-X (X= C, N, O, S and Se) stretching vibrational frequencies in the uracil’s complexes. The changes of thermodynamic properties from the monomer to complexes with the temperature ranging from 200K to 800K have been obtained using the statistical thermodynamic method. It is found that the uracil-H2O complexes can be produced spontaneously from uracil and H2O at low temperature, while the uracil-H2S and uracil- H2Se complexes are produced difficultly.