Mixed reality, as a new human-computer interaction method, has broad application prospects, but whether the mixed reality technology can effectively improve the human-computer effectiveness level in command system remains to be researched. In order to effectively evaluate the human-computer effectiveness level of mixed reality command interface in consideration of the limitations in existing human-computer interface evaluation methods, a multi-indicator comprehensive evaluation method is proposed by designing experiments to compare the task performance, physiological responses, and subjective feelings between the traditional two-dimensional and mixed reality display and interaction systems. By collecting task completion time, eye movement data, physiological indicators, EEG data, and subjective ratings, normalization and weighted processing of both objective and subjective data are carried out to achieve quantitative evaluation of the interface human-computer effectiveness of the two human-computer interaction systems. The multi-indicator comprehensive evaluation method in evaluating the mixed reality human-computer in terface is valid, providing an experimental basis and theoretical support for the scientific evaluation and optimization of the mixed reality command system human-computer interface.