It is not an easy task to construct or verify the validit of an inherently complicated a two-tier misconception test by conventional methods. The aim of this research is to employ homogeneity analysis (Homals) to analyze a two-tier misconception test. Specifically, variable quantification and discrimination measures of the Homals were used to study the homogeneity between variables and the discrimination power of variables in our two-tier misconception test. Our study results showed that the proposed method provided an effective way to provide information about construct underrepresentation and construct-irrelevant variance of a two-tier misconception test in science.