Body size remains a major trait due to its high economic impact for breeding selection. This study was aimed to select high-yielding Jinding ducks based on body size and physiological indicators. A total of 264 Jinding ducks were measured for eleven body size measurements and body weight, as well as seven hormones and four biochemical indicators (high-yielding duck, HYD, n = 132; low-yielding duck, LYD, n = 132). All data were subjected to t-tests and Pearson correlation analysis. The results revealed that HYD exhibited higher levels of gonadotropin-releasing hormone (GnRH), follicle-stimulating hormone (FSH), luteinizing hormone (LH), progesterone (PROG), testosterone (T), estradiol (E2), glucose (GLU), and triglyceride (TG) (P < 0.01) while lower levels of prolactin (PRL) (P < 0.01) compared with LYD. The HYD showed wider pubic spacing, slender necks, and longer keel bones than LYD (P < 0.01). The HYD also had wider body slope length, half-diving depth, chest depth, chest width, and tibia length (P < 0.05). Thus, based on the significant differences in body size and hormone levels, we further investigated the association between them. The result showed that the pubic spacing and neck length were positively correlated with GnRH, FSH, and PROG (P < 0.01) and negatively correlated with PRL (P < 0.05), while the keel bone length was positively correlated with GnRH, FSH (P < 0.01) and E2, PROG (P < 0.05).The half-diving depth was positively correlated with GnRH, E2 (P < 0.01) and LH, PROG (P < 0.05). This study provided breeding strategies and showed that HYD could be selected by wide pubic spacing, long keel bones and slender necks.