This paper studies the computer-assisted model of the difference between the theory and practice of physical education by the information system of the intelligent department. First, multimedia physical education courseware, physical education student learning courseware, physical education information inquiry and exchange, auxiliary physical education teaching research, office automation, etc. A lot of intelligent information guidance is provided, but there is a gap between theory and practice in the process of combining multimedia technology and physical education. The use of intelligent information systems to conduct computer-aided modeling of this gap shows that the gap is about 4.5%~7.9%.