With the advent of knowledge economy, the market has increasingly stricter demands on enterprises, which should have enough flexibility and innovation capacity in order to maintain competitiveness in the fierce market. The core competitiveness of an enterprise is talents. Employees, as the most valuable assets of the enterprise, can not only shorten the innovation cycle and respond quickly to the market, but also achieve the self-satisfaction and value realization if they can effectively exert their innovation ability. This study selects two groups of employees under different corporate cultures as experimental subjects, one enterprise has the perfect mechanism and system of allinvolvement innovation, and the other has no ability of all-involvement innovation. The brain mechanism of employees' decision-making behavior in innovation management is studied by means of scientific research methods and advanced instruments. The results show that the brain structure of the employees with allinvolvement innovation background is different from that of the employees without all-involvement innovation background in the right hemisphere, and the thickness of cortex and the volume of gray matter of the lateral occipital lobe of the right hemisphere are higher than those of the other group. Therefore, the long-term thought training and observation action have produced the plasticity change to the brain, which influences the nerve mechanism of the brain.