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Background This study was conducted to explore the influence of clinical features of rhabdomyosarcoma (RMS) and a refined therapeutic protocol on the therapeutic efficacy and prognosis in children in the past five years. Methods Forty children diagnosed with RMS were retrospectively studied, using a version of the therapeutic protocol refined by Shanghai Children's Medical Center (version 2009.9.1). The patients' demographic characteristics, clinical manifestations, pathological features, therapeutic efficacy, and prognosis were analyzed. Results Of the 40 children, 17 abandoned treatment. Of the remaining 23 cases, two children were rated as low risk, 12 as medium risk, and nine as high risk, and all received treatment. Patients in the low and medium-risk groups had better prognosis than those in the high-risk group, and treated patients had higher survival rates and longer survival than untreated patients. Conclusion Children with RMS should be treated positively. Combined treatment shows better therapeutic efficacy and prognosis. The refined therapeutic protocol seems more effective than the standard treatment, with a significant impact on long-term RMS prognosis.