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Linking the U.S. databases of education and health together—the National Assessment of Educational Progress (NAEP) and the National Survey of Child Health (NSCH), this study explores COVID-19 pandemic impacts and inequalities of whole-child development. It builds on the premise of strength-based, cross-sector approaches to whole-child development and protection for pandemic-affected minority children. It reveals cross-state variations in the amount of losses in student achievement, wellness, and health, wherein pandemic impacts also varied significantly among racial groups by risk and protective factors. The states with more remote learning enrollment during the pandemic suffered relatively larger declines across academic, socioemotional and physical outcomes. In contrast, those states with more protective community environment had relatively smaller losses in child wellness and health.