[Objective] To explore the correct application of the structural equation model and some issues that should be noted when it is applied in the research of mental health.[Methods] The surveys were completed among 448 medical college students by using SCL-90.Structural equation model was used to analyze the data.[Results] The fit indexes of the second-or-der factor model were:Ration=2.65,GFI=0.706 9,AGFI=0.687 6,RMR = 0.078 5,RMSEA = 0.064 5,NFI = 0.685 3,NNFI =0.6890,CAIC =-15.851,CN =167 and all of the load coefficients and other parameters were statistically significant.[Conclusion] It provides a theoretical basis for the research.Certain criteria and application conditions should be followed when structural equation model is applied.