Quantum chemical calculations have been performed to study the molecular geometry, H-1 and C-13 NMR chemical shifts, conformational, natural bond orbital (NBO) and nonlinear optical (NLO) properties of the 2-chloro-5-(2-hydroxyethyl)-4methoxy-6-methylpyrimidine molecule in the ground state using DFT and HF methods with 6-311++G(d,p) basis set. The optimized geometric parameters and H-1 and C-13 NMR chemical shifts have been compared with the experimental values of the title molecule. The results of the calculations show excellent agreement between the experimental and calculated frequencies at B3LYP/6-311++G(d,p) level. In order to provide a full understanding of the properties of the title molecule in the context of molecular orbital picture, the highest occupied molecular energy level (E-HOMO), the lowest unoccupied molecular energy level (E-LUMO), the energy difference (Delta E) between EHOMO and ELUMO, electronegativity (chi), hardness (eta) and softness (S) have been calculated using B3LYP/6-311++G(d, p) and HF/6-311++G(d,p) levels. The calculated HOMO and LUMO energies show that the charge transfer occurs within the title molecule.