Socioeconomic status (SES) affects students’ academic achievement at different levels of an educational system. However, misspecified Hierarchical Linear Model (HLM) may bias school SES estimation. In this study, a partial simulation study was conducted to examine how misspecified HLM model bias school and student SES estimation. The result of this study can be summarized by four important points. First, based on partial simulation procedure, phantom effects of school SES and student SES are real. Second, characteristics of phantom effects are generalized. The stronger the correlation between prior science achievement measure and present science achievement measure, the greater the decrease in both student SES effects and school SES effects. Third, the procedure of partial simulation provides a new angle to conduct theoretical studies (full simulation), which is entirely based on ideal assumption. Finally, the procedure of partial simulation offers researchers a way to create prior student academic achievement measures when they are not available for data analysis.