Currently, the potential role of obesity on semen quality remains unclear. In recent years, alternative anthropometric indices to body mass index (BMI), which can precisely distinguish body fat distribution, have been described to estimate central adiposity. However, the role of neck circumference (NC), a novel index of central adiposity, on semen quality is unknown. This study aims to reveal the potentials of adiposity indices, including NC, in predicting poor semen quality. A total of 4739 male participants between the ages of 17–55 were included in this cross-sectional study. Semen parameters, including sperm concentration, total count, total, progressive and rapid progressive motility and vitality, were divided into two categories according to the WHO classification for male infertility. As anthropometric measurements of obesity, BMI and central obesity indices including waist circumference (WC), hip circumference (HC), waist-to-hip ratio (WHpR), waist-to-height ratio (WHtR) and NC were examined. The predictive potentials of obesity indices for low semen parameters were evaluated by Receiver Operating Characteristics (ROC) curve analysis. The associations of obesity indices with semen parameters were analyzed by binary logistic regression analyze after adjusting potential confounding factors. Patients with lower semen parameters had higher obesity indices than those with normal parameters. All obesity indices have the predictive potentials for low semen parameters. After adjustment for confounders, the strongest associations were found between HC with sperm count parameters, WC and WHtR with sperm vitality and motility parameters and WHpR and NC with rapid progressive motility. Obesity plays an important role in male infertility. Body fat distribution appears to have specific roles on sperm functionality, which may influence different infertility markers. NC is a strong predictor for sperm rapid progressive motility, suggesting a role for male infertility.