There are many papers to discuss the similarities and differences between SEM and MLM on the cross-sectional research when the multilevel studies are growing. But there is few paper to investigate their differences in the longitudinal studies. In this paper, we extend the research of MacCallum et alto the heterogeneous hypothesis and compare the results of SEM and MLM under the heterogeneity and unbalance data settings. The findings analyzed from the repeated measures of 437 companies show that the estimates from the latent growth model of SEM and the linear growth model of MLM are the same under heterogeneity and their outcomes of the unbalanced data are similar. In other words, SEM and MLM are equivalent under heterogeneity assumption and missing data in the longitudinal study.