Independent innovation capability of the SKL is the basic element to build independent innovation system in our country. There are many elements effecting independent innovation capability of the SKL, so we select Lab director as the object, to analyze the relationship between Lab director and independent innovation capability of the SKL with Structural Equation Model. Research shows that, excellent characteristics of directors have appreciable impact on independent innovation capability of the SKL. The academic honor of directors has the greatest influence on it. From the big influence degree to small is: Academic honor, International influence, Age, Unit attribute, Gender.