Trace elements are vital components for healthy growth, development, and physical activity. The aim of this study was to investigate the relationship between trace element (iron, zinc, copper) deficiencies and picky eating behavior, development level, and physical activity level. This cross-sectional study involved 203 children aged 4–7 years; picky eating behavior, development level, and physical activity level were assessed through questionnaires. Zinc deficiency has the highest prevalence (37.4%); 67.5% of the children were assessed as picky eaters. Children with picky eating behaviors, poor development level, or poor physical activity level have significantly lower zinc levels, and higher prevalence of zinc deficiency. Pearson’s correlation coefficient indicated a positive correlation between serum zinc level and development scores (r = 0.221, p = 0.002) and physical activity scores (r = 0.469, p < 0.001). In multivariate analysis, zinc deficiency independently related to picky eating (OR = 2.124, p = 0.037, CI = 1.042–4.312), developmental level (OR = 0.893, p = 0.022, CI = 0.810–0.984), and physical activity level (OR = 0.785, p < 0.001, CI = 0.700–0.879). In conclusion, the prevalence of zinc deficiency in children aged 4–7 was high, especially in picky eaters. Zinc deficiency was significantly associated with low development and poor physical activity in early childhood.