Objective: Several clinical studies were performed on multi-segment intramedullary primary spinal cord tumors. However, no clinical study focused on the relationship between different vertebral segments intramedullary tumors involvement and neurological functions, as well as prognosis of the patients. This prospective study was performed to compare clinical analysis on neurological functions and prognosis of the patients with intramedullary spinal cord primary tumors. Methods: A prospective cohort study was performed in a single medical center, Neurosurgical Department, Peking University Third Hospital. Between Jan. 1, 2010 and Dec. 30, 2015, 135 patients underwent microsurgery for intramedullary primary spinal cord tumors. The intramedullary tumor length occupying 3 or more vertebral body levels was considered as multiple segments intramedullary primary spinal cord tumor, and occupying one or two vertebral body levels considered as seldom segments. Preoperative and postoperative functions were assessed using IJOA (improved Japanese orthopaedic association) scoring system, and analyzed using the appropriate statistical tests. Results: Among the 135 patients, 52 cases had seldom segments intramedullary primary spinal cord tumors, and 83 cases had multiple segments. In the seldom group, 32 (62%) patients presented with normal urine and stool function, 8 (15%) patients with severe dysfunction, 7 (14%) with slight dysfunction, and 5 (9%) with incontinence, and 30 (58%) patients demonstrated various degrees of limbs weakness. The preoperative IJOA scores of the patients were 16.9±2.4. The postoperative IJOA scores at the end of 3 months were 16.6±2.3. The current IJOA scores until the end of the follow-up were 17.5±4.4. In the multiple group, 37 (45%) patients presented with normal urine and stool functions, 26 (31%) patients with slight dysfunction, 11 (13%) with severe dysfunction, and 9 (11%) with incontinence, and 62 (75%) patients demonstrated various degrees of limbs weakness. The preoperative IJOA scores of the patients were 15.6±3.4. The postoperative IJOA scores at the end of 3 months were 15.5±3.8. The current IJOA scores until the end of the follow-up were 16.9±5.8. The difference of presenting urine and stool dysfunction (Z=-1.35, P=0.18) was not statistically significant between the different patient groups. However, the difference of presenting limbs weakness (Z=-2.06, P=0.04) was statistically significant between the two groups. Most patients with multiple segment intramedullary tumors suffered from various limbs weakness. The difference of the preoperative IJOA score (P=0.02) and the postoperative early IJOA score (P=0.004) of the patients was statistically significant between the seldom and multiple segments groups. Preoperative and early postoperative neurological function of the patients was better with seldom segments tumor than with multiple segments tumor. Most patients with multi-segment intramedullary tumors experienced various limbs weakness. However, the difference of long-term neurological function (P=0.12) between the seldom and multiple segments groups was not statistically significant. The neurological function of the patients with multiple segments intramedullary tumor was remarkably improved after physical therapy. Conclusion: Perioperative neurological function of the patients with seldom segments primary tumor was superior to that of the patients with multiple segments primary tumor, especially for limb strength. The neurological function of the patients with multiple segments intramedullary primary tumor was remarkably improved after physical therapy during long-term follow-up.