This study aimed to compare the effects of 12 weeks of functional strength training combined with aerobic training (TG) and traditional resistance training combined with aerobic training (CG) on the body composition, physical fitness, and movement quality of obese adolescents. Forty participants were randomly assigned to either the TG group (n = 20) or the CG group (n = 20). Each group underwent training five times per week, lasting 120 min each time, over a total period of 12 weeks. All participants followed a strict dietary program. Anthropometric parameters, body composition, physical fitness, and movement quality were evaluated at baseline and after intervention. A two-way repeated measures ANOVA observed a significant interaction between time and group for body mass (p = 0.043), body fat percentage (p = 0.045), body mass index (p = 0.025), neck circumference (p = 0.01), chest circumference (p = 0.027), left-hand grip strength (p = 0.043), right-hand grip strength (p = 0.048), standing broad jump (p = 0.044), and total Functional Movement Screen score (p = 0.003), and the improvement was greater for TG in comparison to CG. TG was found to be more effective than CG in enhancing body composition, physical fitness, and movement quality in obese adolescents.