The use of mathematical modeling and simulation in engineering is rapidly increasing since modern products are increasingly complex and heterogeneous. Consistency analysis of simulation model is a crucial subject of multi-domain modeling of complex physical systems. In this paper, a structural analysis method based on graph theoretical approaches is presented. The method can not only determine whether a simulation model is consistent or not, but also decompose the overall system of equations into three distinct parts: over-constrained, under-constrained, and well-constrained part. A methodology is also proposed for detecting and repairing over-constrained and under-constrained situations. Equations and variables that cause the inconsistencies can be automatically detected and isolated without solving the system of equations, and meaningful repairing messages for users are given. The methodology can considerably enhance the error finding and correcting process by providing a broad range of errors, and is implemented in a modeling and simulation tool, named MWorks.