To identify seedling traits closely associated with drought resistance and to screen for drought-tolerant germplasm, 202 cotton varieties (lines) were evaluated under controlled indoor conditions using a nutrient soil cultivation method. Seedling-stage traits measured included plant height, cotyledon node diameter, true leaf number, chlorophyll content, and fresh and dry biomass of both shoots and roots. Drought resistance was assessed using drought resistance coefficients for each trait, followed by descriptive statistics, principal component analysis (PCA), partial correlation analysis, and comprehensive evaluation via the entropy weight method. PCA and partial correlation analysis revealed that plant height, cotyledon node diameter, aboveground fresh weight, and underground fresh weight were strongly associated with drought resistance at the seedling stage. The comprehensive drought resistance index (D-value) classified the 202 cotton lines into four categories: highly drought-resistant, moderately drought-resistant, drought-sensitive, and highly drought-sensitive. Physiological assays indicated that malondialdehyde (MDA) content in drought-resistant lines first increased and then declined with prolonged drought stress, while it continued to increase in sensitive lines. In contrast, proline (Pro) content and superoxide dismutase (SOD) activity increased steadily in drought-resistant lines but showed negligible changes in sensitive lines. These four morphological traits and three physiological indicators represent reliable criteria for evaluating drought resistance in cotton seedlings. Four highly drought-resistant and thirteen moderately drought-resistant lines were identified, providing valuable germplasm for genetic improvement of drought tolerance in cotton.