In this study, we construct a method for evaluating thinking and judgment as intellectual productivity of system engineers, with a particular focus on a supporting system that the engineers engaged in software development. This method can be applied in two ways. The first application is an approach to evaluate the skill of system engineers. This method can not only evaluate the engineer's aptitude by scoring intellectual productivities but can also analyse tendencies related to the skill of system engineers by using proportions of each control processes and time-series graphs. The second application is an approach to improve the tools and manuals of the development environment. By comparing time-series graphs of the thinking process with operating logs, we can identify the specific point where system engineers have fallen into scrambled control processes so that we can specifically identify the problem in the corresponding instructions and manuals, which should result in improvements in development environment tools.