Abstract: Aiming at the difficulty and complexity of system structure analysis, a new system structure analysis arithmetic with reachable effect factor is presented. The effect matrix is obtained based on qualitative estimation and experimentation analysis firstly, then the administrative levels of system structure is actualized based on emendatory effect matrix in which unimportant elements judged by center degree and cause degree are omitted. Finally system structure analysis model with reachable effect factor is established. Experimental results show that, the proposed arithmetic could realize the system structure analysis effectively based on the fact that unimportant elements and their effect relations are omitted, and its improvement and practicality lie in the fact that it not only reduces the complexity of computing reachable effect matrix by using improved Boolean algebra rules, but also presents the effect degree of important elements quantificationally.