Hydroponics is currently one of the primary methods for soilless cultivation. Although the phenotype and quality of vegetables differ between hydroponic and soil-based systems, limited research has been conducted on the selection and breeding of pakchoi cultivars specifically suited for hydroponics. In this study, principal component analysis (PCA) and cluster analysis were performed on the commercial traits, agronomic characteristics, and nutritional quality of 20 pakchoi parental lines grown under hydroponic conditions to classify and screen suitable germplasm for breeding. PCA reduced the 11 agronomic traits into two independent principal components, accounting for a cumulative contribution of 79.22%. Cluster analysis grouped the 20 parental lines into four categories based on the composite scores of agronomic traits and nutritional quality. Group 3 was selected for breeding programs aiming to develop high-yielding cultivars with a desirable morphology. For breeding targets emphasizing darker leaves and petiole coloration, Group 4 presented the most suitable germplasm. Group 1 was ideal for enhancing nutritional quality by offering parent lines rich in calcium, magnesium, vitamin C, and amino acids. Alternatively, Group 2 contained lines with high levels of soluble proteins, amino acids, and soluble sugars.