This paper aims to explore the application research of collaborative design theory in the design of military information systems. The participants involved in the design of military information systems and their needs are combed and analyzed; the collaborative design process of military information systems is constructed; the subjects are invited to participated in experiments and questionnaires. It adopts two approaches, including the data analysis information done by means of eye-moving experiments and the data accuracy verification according to the questionnaire data, to evaluate the feasibility of military information system design based on collaborative participation. Experiments show that collaborative design can obtain more complete design requirements by increasing the participants’ involvement in the design process, improve the decision-making efficiency of military information system, and optimize the operating experience.