Background: RIOM is a common side effect of radiotherapy for head and neck cancer patients, however, no standard and effective treatment existed so far. WC03 is an oily Traditional Chinese Herbal Medicine recipe for external-use in mouth, which had been utilized to treat RIOM in China-Japan Friendship Hospital for more than ten years. This trial aimed to investigate the safety and efficacy of WC03 in treating RIOM. Methods: Between May 2017 and June 2018, we conducted a multicenter, non-randomized controlled trial within 7 hospitals in China. Inclusion criteria included head and neck cancer patients who developed RIOM (≥ grade II) undergoing radiotherapy or after radiotherapy (within 6 months). They were assigned to different groups based on their willingness. Patients in treatment group were treated by WC03, which was daily applied to the oral mucosa for 30 min twice a day. Patients in control group were treated with Kangfuxin (Periplaneta americana) Lotion combined with conventional treatment such as vitamin B12 and rhGM-CSF. The interventions lasted for 2 weeks. The primary outcome was overall effective rate, which was calculated through changes of radio-induced oral mucositis grade before and after interventions (according to National Cancer Institute Common Toxicity Criteria). Secondary outcome was oral pain which was measured by Numeric Pain Rating Scale. Results: 48 eligible participants were enrolled, 24 in treatment group and 24 in control group, respectively. 2 patients in treatment group were withdrawn from the study in the first week because of developing secondary infection and treatment got changed. Thus, 22 were included at the terminal of the study. All the 24 participants in control group were included. After the intervention, the overall effective rate was 95.45%(21/22) in the treatment group, which was significantly higher than that of 70.83% (17/24) in the control group (p = 0.049). Similarly, 86.36%(19/22) of the participants in treatment group got cured, which was significantly higher than that of 45.83%(11/24) in the control group(p = 0.007). There is a trend that oral pain relief rate in the treatment group was higher than that of the control group, but not statistically significant (100.00% vs. 87.50%, p = 0.210). Patients in treatment group used less time to get relieved from RIOM than control group (5 vs. 8 days, p < 0.001). No adverse event had been observed in both two groups. Conclusions: WC03 is safe and effective in treating radiotherapy-induced oral mucositis. RCT is necessary in future studies.