Background: The decline in adolescent health-related physical fitness has become a global concern. School physical education programs play a crucial role in enhancing physical fitness and promoting students’ overall health. Objective: This study aims to compare the effects of high-intensity interval jump rope training (High-Intensity Interval Training-Jump Rope, HIIT-JR) and moderate-intensity continuous jump rope training (Moderate-Intensity Continuous Training-Jump Rope, MICT-JR) on health-related physical fitness in adolescents, providing empirical evidence for refining school physical education curricula. Methods: A randomized controlled trial was conducted with 120 high school students, who were randomly assigned to the HIIT-JR group, the MICT-JR group, or an unstructured activity control group (FT). The intervention lasted 12 weeks within the framework of school physical education. The HIIT-JR group performed 1-minute high-intensity jump rope exercises (75%–90% of maximum heart rate), alternating with 1-minute rest intervals, for a total of 11 rounds per session. The MICT-JR group performed continuous moderate-intensity jump rope exercises (55%–74% of maximum heart rate) for 11 minutes per session. Health-related physical fitness was assessed using the 20-meter shuttle run (cardiorespiratory endurance), standing long jump (muscular strength), sit-ups (muscular endurance), sit-and-reach test (flexibility), and body mass index (BMI; body composition). Data were analyzed using SPSS 23.0, with two-way repeated measures ANOVA and correlation analysis used to evaluate training effects. Results: Both HIIT-JR and MICT-JR effectively improved health-related physical fitness, though their effects differed across various fitness components. Cardiorespiratory endurance: The HIIT-JR group exhibited rapid improvements within the first 6 weeks (p < 0.01), whereas the MICT-JR group showed more gradual gains, primarily between Weeks 6 and 12 (p < 0.05). Muscular strength: The HIIT-JR group demonstrated significant improvements in standing long jump performance after 6 weeks (p < 0.01), while the MICT-JR group showed minimal changes (p > 0.05).Muscular endurance: The MICT-JR group exhibited significant improvements in sit-up performance after 12 weeks (p < 0.01), whereas no significant changes were observed in the HIIT-JR group (p > 0.05).Flexibility: Both training groups showed slight improvements, but the differences were not statistically significant compared to the control group (p > 0.05).BMI: The MICT-JR group experienced a significant reduction in BMI after 12 weeks (p < 0.01), whereas no significant changes in body weight regulation were detected in the HIIT-JR group (p > 0.05). Conclusion: Jump rope training of different intensities has varied effects on different components of health-related physical fitness. HIIT-JR leads to faster improvements in cardiorespiratory endurance and muscular strength, while MICT-JR is more effective for enhancing muscular endurance and reducing BMI. A structured integration of both training modalities into physical education programs, customized according to students’ individual fitness profiles, may optimize adolescent fitness outcomes and long-term health benefits.