In this study, structural equation modeling (SEM) is applied to an instrument assessing students' understanding of chemical change. The instrument comprised items on understanding the structure of substances, chemical changes and their interpretation. The structural relationships among particular groups of items are investigated and analyzed using confirmatory procedures. In addition, three psychometric cognitive variables, namely logical, convergent and divergent thinking are involved in the SEM analysis and their effects on students' performance estimated. Specifically, three models are tested: a confirmatory factor model, a multiple-indicator multiple-cause (MIMIC) model and path analysis. The SEM analysis showed that the cognitive variables, along with students' achievements in understanding the structure of substances and their changes, sufficiently explained students' ability to interpret chemical phenomena, providing additionally their direct and indirect effects. The theoretical analysis and the interpretation of the results contributed significantly to an understanding about the role of the above individual differences in learning secondary school chemistry. Implications for science education are also discussed.