In view of the problems existing in the teaching of Mathematics Foundations of Information Security, such as emphasizing theory but neglecting practice, combined with the concept of engineering education certification and emerging engineering education teaching reform, this paper combs the knowledge points and learning context of Mathematics Foundations of Information Security, puts forward a new teaching mode of Mathematics Foundations of Information Security with algorithm as the core, and gives the teaching content, organization form and assessment method. Thus, it improves the students' learning interest and practical ability, and improves the achievement of graduation requirements.