At present, there are some problems in color wheat breeding, such as unsystematic germplasm evaluation, unclear coordination mechanism of agronomic traits, and lack of quantitative basis for screening excellent parents. In order to clarify the phenotypic variation, trait association characteristics and comprehensive performance of colored wheat germplasm resources in Huang-huai wheat area, and improve the selection efficiency of breeding parents, 40 colored wheat germplasms and 1 common wheat germplasm control (ZM18) were used as materials in this study. Nine agronomic traits such as plant height, spike length, flag leaf traits and spikelet number were investigated at mature plant stage, and genetic variation, comprehensive evaluation including principal component and cluster analysis were carried out. The results showed that the 40 colored wheat germplasm resources had abundant variation and specific characteristics. The variation coefficient of nine agronomic traits ranged from 10.750% to 120.147%, and the diversity index ranged from 1.083 to 2.057. More than 77.78% of agronomic traits had variation coefficients greater than 15%, and diversity indices greater than 1.8. The overall performance of colored wheat is characterized by long flag leaf, large flag leaf angle, many fertile spikelets, and short peduncle and exposed peduncle. Correlation analysis indicates that the number of fertile spikelets is significantly correlated with most traits. Among them, it was significantly positively correlated with ear length (r=0.50) and flag leaf width (r=0.53), while ear length was significantly or highly significantly positively correlated with plant height (r=0.33) and flag leaf length (r=0.58), and plant height was highly significantly negatively correlated with flag leaf width (r=-0.47). Principal component analysis simplified the nine traits into three principal components, which could explain 75.412% of the trait information. Plant height, ear length, and flag leaf angle were the core indicators. The comprehensive evaluation value (D value) was used to assess the overall performance of each germplasm, with a higher D value indicating better overall performance. Thirteen colored wheat germplasm resources with D values greater than D_CK (0.523) were screened out, among which KDH1, LLM1, ZHM1, and LHM1 had relatively short plant heights at 66.67, 85.50, 82.50, and 80.88 cm, respectively, which could be used as candidate parents. When the genetic distance was 5.78, the 41 test materials can be divided into five major categories, with Group III having the most germplasm resources, and Group V having more germplasm resources and a larger mean D value (0.638). In summary, the agronomic traits of 40 colored wheat germplasm resources had rich variations and clear characteristics. When breeding new varieties, attention should be paid to the coordinated relationship among plant height, ear length, flag leaf length, flag leaf width, and number of fertile spikelets. Cluster analysis further clarified the characteristics of germplasm resources in different groups. Four candidate parents with larger D values and shorter plant heights were screened out. This provides a reference for high yield, lodging resistance, ideal plant type breeding or improvement, the utilization of agronomic traits, and the selection of parents of colored wheat varieties. Subsequent multi-dimensional accurate evaluation can be carried out in combination with yield and quality traits.