Objective Anthropometric variants in prepubertal boys with hypospadias were assigned and assessed to illustrate anatomical malformation. Methods A total of 516 prepubertal (Tanner grade Ⅰ) boys with hypospadias who were admitted to three medical centers between March 2021 and December 2021 and met the selection criteria for primary surgery were selected. The age of the boys ranged from 10 to 111 months, with an average of 32.6 months. Hypospadias were classified according to the location of the urethral defect, 47 cases (9.11%) of the distal type (the urethral defect is in the coronal groove or beyond), 208 cases (40.31%) of the middle type (the urethral defect is in the penis body), and 261 cases (50.58%) of the proximal type (the urethral defect is at the junction or proximal side of the penis and scrotum). The following indexes were measured: penis length before and immediately after operation, reconstructed urethral length, and total urethral length. Morphological indicators of the glans area, including preoperative height and width of glans, AB, BC, AE, AD, effective AD, CC, BB, the urethral plate width of the coronal sulcus, and postoperative height and width of glans, AB, BE, and AD. In which point A is the distal endpoint of navicular groove, point B is the protuberance lateral to the navicular groove, point C is the ventrolateral protuberance of the glans corona, point D is the dorsal midline point of the glans corona, and point E is the ventral midline point of the coronal sulcus. The foreskin morphological indicators, including the foreskin width, inner foreskin length, and outer foreskin length. The scrotal morphological indicators, including the left, right, and front penile to scrotum distance. The anogenital distances, including anoscrotal distance 1 (ASD1), ASD2, anogenital distance 1 (AGD1), and AGD2. ResultsThe penis length of the distal, middle, and proximal types decreased successively before operation, the reconstructed urethral length increased successively and the total urethral length decreased successively, these differences were all significant (P<0.05). The height and width of the glans of the distal, middle, and proximal types significantly decreased successively (P<0.05), but the height/width of the glans was generally close; AB value, AD value, and effective AD value significantly decreased successively (P<0.05); there was no significant difference in BB value, urethral plate width of the coronary sulcus, and (AB+BC)/AD value between the groups (P>0.05). There was no significant difference in the width of glans between the groups after operation (P>0.05); AB value and AB/BE value increased successively, and AD value decreased successively, these differences were all significant (P<0.05). The inner foreskin length in the 3 groups significantly decreased successively (P<0.05), while the outer foreskin length had no significant difference (P>0.05). The left penile to scrotum distance of middle, distal, and proximal types significantly increased successively (P<0.05). ASD1, AGD1, and AGD2 significantly decreased from distal type to proximal type successively (P<0.05). The other indicators’ differences were significant only between some groups (P<0.05).Conclusion The anatomic abnormalities of hypospadias can be described by anthropometric indicators, which can be used as the basis for further standardized surgical guidance.