Background: Although poorly differentiated is rare in head and neck squamous cell carcinoma (HNSCC), its prognosis are worse with high rate of local recurrence and distant metastasis (DS). Therefore, this study hopes to carry out prospective clinical research on different treatment options for poorly differentiated patients and explore the treatment scheme more suitable for these patients. Methods: This study is a prospective cohort study. We selected patients with poorly differentiated carcinoma in larynx or hypopharynx (stage I-IV, T1-4a, N0-2, M0). The intervention treatment methods for stage I-II patients are as follows: surgery, induction chemotherapy (IC) + surgery, surgery + adjuvant therapy; The intervention treatment methods for stage III-IV patients are as follows: surgery, IC + surgery + adjuvant therapy, surgery + adjuvant therapy. The patients were followed up for at least 1 year, and the disease progression and survival were counted. Results: From September 2016 to October 2020, 62 patients were included (29 patients in stage I/II and 33 patients in stage III/IV). We found that there was no significant difference in survival between treatment groups in stage I/II patients [overall survival (OS): P=0.447; progression free survival (PFS): P=0.504], but the surgery + adjuvant treatment group had a significant advantage in 3-year OS (100%). In stage III/IV patients, there were significant differences in DS, OS and PFS between different treatment groups (DS: P=0.013; OS: P=0.021; PFS: P=0.020). Among them, the survival rate of IC + surgery + adjuvant treatment group was the best, with 3-year OS of 78%. Conclusions: Our study found that postoperative radiotherapy may improve the OS rate of patients with early (stage I/II) poorly differentiated HNSCC; For advanced patients (stage III/IV), surgery combined with IC and postoperative adjuvant radiotherapy may better control DS and improve the survival rate. However, our study draws the above conclusions based on small sample data, and we will continue to summarize and expand the sample size for verification.