Since the traditional single tree index can not fully describe credibility of system of systems, especially when there are interoperation relationships within it, we have proposed a new hybrid index system construction methodology. We first establish a common evaluation index library, which within certain range, can be tailored according to the different application area. Using this as a base, we construct a multi-dimension assessment index system from the views of system function, operation effect and technique architecture. Based on simulation experiment data, we can mine the interoperation relationships among existing indexes, and construct a credibility assessment method for these relationships to establish the dynamic and networked index system. This hybrid index system construction methodology can build reference and support for research on credibility assessment for simulation system of complex system of systems.