For the uracil-BX3 (X = F, Cl) systems, geometries and binding energies have been calculated by using the Lee-Young-Parr correlation functionals (B3LYP) method of density functional theory (DFT) and the second-order Moller-Plesset (MP2) method of ab initio at the 6- 311+G* or 6-311++G* basis set. Four isomers were found for each system, and then the single-point energy evaluations were performed using the larger basis sets of (6-311+G(2df,p) and aug-cc-pVDZ with DFT method. In the most stable isomer of uracil-BF3 or uracil-BCl3, the boron atom of BX3 (X = F, Cl) connects to the carbonyl oxygen O7 of uracil with a stabilization energy of –46.56 or –31.10 kJ/mol at the B3LYP/6-311+G* level (BSSE corrected). The analyses for combining interaction between BX3 and uracil with the atom-in-molecule theory (AIM) and natural bond orbital method (NBO) have been performed. The results indicate that all isomers were formed with σ-p type interactions between uracil and BX3, in which the carbonyl oxygen offers its lone pair electrons to the empty p orbital of boron atom and the concomitances of charge transfer from uracil to BX3 occur. Moreover, there exists one or two hydrogen bonds in most isomers of uracil-BX3 system and these hydrogen bonds contribute to the stability of the complex systems. Frequency analysis suggests that the stretching vibration of BX3 undergoes a red shift in complexes. Uracil-BF3 complex is more stable than uracil-BCl3 although the distance of B–O is shorter in the latter. Besides, the conversion mechanisms between different isomers of uracil-BF3 have been obtained. For the uracil-BX3 (X = F, Cl) systems, geometries and binding energies have been calculated by using the Lee-Young-Parr correlation functionals (B3LYP) method of density functional theory (DFT) and the second- order Moller-Plesset (MP2) method of ab initio at the 6- 311 + G * or 6-311 ++ G * basis set. Four isomers were found for each system, and then the single-point energy evaluations were performed using the larger basis sets of (6-311 + G (2df, p) and aug-cc-pVDZ with DFT method. In the most stable isomer of uracil-BF3 or uracil-BCl3, the boron atom of BX3 (X = F, Cl) connects to the carbonyl oxygen O7 of uracil with a stabilization energy of -46.56 or -31.10 kJ / mol at the B3LYP / 6-311 + G * level (BSSE corrected). The analyzes for combining interaction between BX3 and uracil with the atom-in-molecule theory (AIM) and natural bond orbital method (NBO) have been performed. The results indicate that all isomers were formed with σ-p type interactions between uracil and BX3, in which the carbon yl oxygen offers its lone pair electrons to the empty p orbital of boron atom and the concomitances of charge transfer from uracil to BX3 occur. Furthermore, there exists one or two hydrogen bonds in most isomers of uracil-BX3 system and these hydrogen bonds contribute to the stability of the complex systems. Frequency analysis suggests that the stretching vibration of BX3 undergoes a red shift in complexes. Uracil-BF3 complex is more stable than uracil-BCl3 although the distance of B-O is shorter in the latter. conversion mechanisms between different isomers of uracil-BF3 have been obtained.