A hydrogenation method for increasing the yield of cyclohexane-1,4-dicarboxylic acid diisooctyl ester is provided. The hydrogenation method uses a hydrogenating reaction tank, which is equipped with a hollow-shaft gas-introducing mixer having air-extracting, air-exhausting and mixing functions, to allow hydrogen gas to be uniformly dispersed in a reaction solution. A ruthenium-on-alumina (Ru/Al2O3) hydrogenation catalyst can be used for carrying out a hydrogenation reaction under gentle conditions. Therefore, the hydrogenation catalyst can be used in a reduced amount, the risk of side reaction(s) can be reduced, and the yield of cyclohexane-1,4-dicarboxylic acid diisooctyl ester can reach at least 99% with a cis isomer proportion of at least 85.0%. The hydrogenation method shows extremely high economic benefit.