To investigate the clinicopathological features, diagnosis, treatment and prognosis of primary rectal squamous cell carcinoma (SCC), a case of primary rectal SCC was collected, Histopathological features and immunophenotype were observed. The related literatures were reviewed. A male patient, 40 years old, stool with blood without obvious reason. Enteroscopy showed “protuberant rectal lesions, nature to be investigated”. After radiotherapy and chemotherapy, the diseased intestinal segment was resected surgically. In general, 3 cm ×3 cm ×3 cm uplift hard area was visible to the naked eye. The section was gray and hard. Microscopically, a large number of nest-like tumor cells infiltrated into the parenteral adipose tissue. The tumor cells were moderately to poorly differentiated, some of them were round and oval, with abundant and pale cytoplasm, keratinization was seen in single cells, and some of them were poorly differentiated, spindle-shaped, with thick chromatin. The cell heteromorphism was obviously accompanied by a large number of pathological mitosis and a small amount of lymphocyte infiltration. Immunohistochemistry showed that the tumor cells were positive for CK5/6, P16, P63, P40, CAM5.2, Ki-67 LI was about 50%. Primary rectal SCC is rare and has a poor prognosis. Its characteristic histomorphology and immunohistochemical phenotype are helpful to the diagnosis and differential diagnosis. There is no accepted best treatment for this disease. Further studies should be made from the aspects of pathogenesis, diagnosis and treatment.