Quantum chemical calculations have been performed to study the molecular geometry, 1H and 13C NMR chemical shifts, conformational, natural bond orbital (NBO) and nonlinear optical (NLO) properties of the 2-chloro-5-(2-hydroxyethyl)-4- methoxy-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 1H and 13C 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 (EHOMO), the lowest unoccupied molecular energy level (ELUMO), the energy difference (DE) between EHOMO and ELUMO, electronegativity (χ), hardness (η) 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.