By identifying the ability of drought resistance and screening indices at flowering and boll setting stage of upland cotton(Gossypium hirsutum L.), this study aimed to provide the materials and a theoretical basis for drought-resistant breeding and cultivation. 153 varieties (lines) were planted under normal irrigation and drought stress conditions, while the drought treatment was conducted by using reduced water at flowering and boll setting stage. Several agronomical traits, including means of plant height, lint percentage, single boll weight, the first node of fruit branch, initial internodes of fruiting branch, effective boll number, fruit branch number, cotton seed yield, fiber length (mm), specific breaking length, uniformity and micronaire, were measured. The statistical analysis was conducted by combination with the comprehensive drought coefficient, membership function, principal component analysis, association analysis and clustering analysis. The agronomic traits of upland cotton varieties (lines) represented large variation upon drought stress treatment. The ranks of drought resistance of tested upland cotton varieties (lines) based on D value. According to clustering results of D value, these upland cotton varieties (lines) could be divided into five types. Type 1(Strongly resistant) included 5 cotton varieties, type 2(Resistant) had 35 cotton varieties, type 3(Modetarely resistant) had 57 cotton varieties, type 4(Modetarely sensitive) had 56 cotton varieties and type 5(Sensitive) had 1 cotton variety. The yield of tested upland cotton varieties (lines) had significant and positive correlation with D (drought resistance comprehensive evaluation) value, CDC (comprehensive drought resistance coefficient) value and WDC (weight drought resistance coefficient) value. Finally, we identified two varieties Israel 1101 and yanzao 2, which were identified as drought resistant and sensitive upland cotton varieties at flowering and boll setting stage, respectively. Plant height, yield, single boll weight, effective boll number and height of the first branch could be used as the identification indices for drought resistance in upland cotton germplasm resources at flowering and boll setting stage.