Binding energy calculations of flurbiprofen to the binding pocket of the cyclooxygenase (COX) enzyme were performed based on quantum chemical calculations. The interaction energies between flurbiprofen and two types of COX binding sites were studied. Quantum chemical calculations were used, based on the B3LYP hybrid functional and the MP2 method, with 6-31G(d) and 6-31G(d,p) basis sets. The results show that the main interaction between flurbiprofen and two COX isozymes (COX-1 and COX-2) is due to Arg120. In addition, selective SC558 COX-2 inhibitor was also compared. It was found that repulsive interaction plays a significant role in its inhibition of COX-2. ONIOM2(B3LYP/6-31G(d):PM3) calculations indicate that flurbiprofen interacts via moderate hydrogen bonding with Arg120 in the COX-2 binding site, while no hydrogen bond was detected with either Tyr355 or Val523. The ONIOM2 method can be used to describe the specific interaction of the inhibitor and is helpful in designing a specific COX inhibitor.