Engineering structure was an important main course of engineering management specialty. It is also the emphasis and difficulty of teaching reform about the course system of that speciality. This paper introduced the characteristics of engineering structure and summarized the existing problems during the teaching process of that course. Through analyzing the school-running characteristics of independent college, specialty characteristics of engineering management and the practical research of the teaching, this paper researched and proposed several course teaching reform methods which included optimizing the course contents, reforming teaching methods and teaching means, enhancing practical teaching link, using the comprehensive sets of evaluation mechanism and improving the teachers’ quality.