There are some issues that should be solved like load shock, vibration, and uneven load distribution during transmission of involute spur gears. However, common modification methods such as axial modification as well as profile modification could not solve these problems once for all. Hence, a novel method of comprehensive modification was proposed, and the evaluation methodology of transmission performance was drawn up too. Changing modification parameters can control transmission performance of gear unit, which can generate many different modification ways. Besides, based on the orthogonal experiment method and evaluation methodology, optimal modification ways can be chosen for gear pairs working in different conditions. Taking a set of spur gear pair as an example, an ideal modification way was obtained. In addition, analysis results verified that conducting comprehensive modification could enhance the meshing performance once for all.