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Fully conditional specification (FCS) is an increasingly used multiple imputation approach to treat missing data with nested structure. However, practices associated with the employing of FCS on missing data in multilevel regression modeling (MRM) are problematic due to the lack of empirical research. Also, little is known about how the complexity of Level-2 missingness and unbalanced group size affect FCS’s performance. A Monte Carlo simulation was employed here to investigate the effects of FCS to treat level-2 missing data in MRM with unbalanced groups. The results showed that FCS performed well in most conditions, but is currently not suitable for recovering parameters and capturing random effects in low ICC, sample group size combined with high missing rate conditions.