In recent years, improving the engine thermal efficiency is strongly required. To enhance the engine thermal efficiency, it is important to improve the engine anti-knock quality. Technologies for modifying engine cooling have been developed to improve anti-knocking quality of engines. However, excessive improvement of engine cooling leads to an increase in cooling heat loss. Therefore, it is necessary to clarify the effects of the temperature of each part of the engine such as engine head-cylinder, cylinder-liner, and piston on knocking and cooling heat loss. In this paper, computer aided engineering (CAE) is used to predict the effects of each part of the engine on engine knocking and cooling heat loss. Firstly, the amount of heat energy that air-fuel mixture receives from engine cylinder-head, cylinder-liner, and piston is calculated during the intake stroke. The result shows that the cylinder-liner contributes largest heat energy to air-fuel mixture, especially the exhaust side. It indicated that the cylinder-liner has a maximum effect on the rise in temperature of the air-fuel mixture. Secondly, the amount of heat energy discharged from the combustion gas to engine cylinder-head, cylinder-liner, and piston was calculated during the expansion stroke. The result shows that the cylinder-liner receives the smallest heat energy from the combustion gas. These CAE results indicate that cooling the upper part of the cylinder-liner on the exhaust side is an effective way to improve anti-knock quality. This CAE was validated with a single-cylinder engine equipped with a total of fourteen independent cooling water paths and about 150 thermocouples. Thermal flow pattern in the engine and the effect of structural temperature in the combustion chamber on knocking were investigated. The test result shows an agreement with the CAE result, indicating the effectiveness of cooling of the liner on anti-knock quality.