Natural systems are essentially complex. In most cases, fully understanding natural systems requires the capacity to examine simultaneous influences and responses among multiple interacting factors. Compared with traditional multivariate methods, structural equation model (SEM) could specify the causal or dependent relationships among variables using the prior knowledge of researchers before conducting relevant experiments, i.e. initial models. SEM could not only identify the individual path coefficient for each relationship, but also estimate the whole model fit to determine whether to revise the initial models. We attempt to introduce SEM from the following aspects: definition and types of variables in SEM, detailed procedures for how to analyze data through SEM, some applications of SEM in ecology and recommended software. We encourage more researchers to apply SEM in ecological data analyses in order to improve understanding of natural systems and advance the field of ecology.