This study was motivated by the National Assessment of Educational Achievement (NAEA) involving a complex survey design for sampling. The goal of the study was to explore the benefit of weighted analysis in multilevel modeling. Large-scale data such as the NAEA data are often analyzed in multilevel analyses to reflect the nested data structure. A simulation study was conducted incorporating different conditions. Multilevel analysis results were compared without weights, with basic design weights, and with a raked weight, which were generated in consideration of explicit and implicit stratification variables with auxiliary variables. Simulation also compared the analysis results by varying the number of classes per school in a stratified cluster sampling design. In summary, substantial benefits were not observed in weighted multilevel analysis compared to unweighted multilevel analysis, although the weighted descriptive statistics were close to the population means relative to the unweighted descriptive statistics. These findings may help provide scientific evidence for the use of sampling weights in analyses with large-scale educational data.