The purpose of this study was to establish the association between total and segmental body composition (BC) variables and anaerobic performance and to create optimal models that best predict such performance in CrossFit® (CF) athletes. Fifty athletes, 25 males and 25 females (age: 33.26 ± 6.81 years; body mass: 72.57 ± 12.17 kg; height: 169.55 ± 8.71 cm; BMI: 25.06 ± 2.31 kg·m−2) were recruited to participate and underwent BC analysis using dual-energy X-ray absorptiometry (DXA) and an all-out laboratory test on a cycle ergometer (Wingate) to determine their anaerobic performance. The results show a significant correlation between BC values and performance, ranging from moderate (r = -0.34, p = 0.015) to near-perfect (r = 0.96, p < 0.01). Furthermore, the created performance prediction models exhibited predictive capacities ranging from 19% (p = 0.017) to 93% (p < 0.001). All prediction models were created using total or segmental lean mass variables, excluding others. BC and performance variables found significant differences between males and females. The findings demonstrate that BC variables are crucial indicators of anaerobic performance in CF athletes. Professionals responsible for athlete performance should use this information to monitor athletes and design training programs.