Objective: To explore the changes of serum neuron-specific enolase (NSE) and myelin basic protein (MBP) in children with cerebral palsy at high altitude during comprehensive rehabilitation and their clinical significance. Methods: A clinical randomized controlled study design was used to select 144 children with cerebral palsy who were diagnosed and treated in the Rehabilitation Center of Xining Traditional Chinese Medicine Hospital of Qinghai Province from June 2018 to October 2019, including 83 males and 61 females, aged 3-5 years old. According to the order of admission, the random number table was used to divide into a conventional treatment group (n=72, 40 males and 32 females) and a comprehensive treatment group (n=72, 43 males and 29 females). The conventional treatment group was treated with conventional rehabilitation. The comprehensive treatment group was treated with monosialotetrahexose ganglioside sodium on the basis of conventional rehabilitation. In addition, 30 healthy children aged 3-5 years, 16 males and 14 females, were selected as the control group during the physical examination of the Pediatrics Department of Xining Hospital of Traditional Chinese Medicine, Qinghai Province. The serum levels of NSE and MBP in each group were detected, and the children's GMFM-88 scores were evaluated before and after treatment. The SPSS19.0 software was used for statistical analysis, the count data was tested by χ2. Results: The serum NSE and MBP levels of the control group were (5.96±0.80), (0.71±0.15) μg/L. Before treatment, the serum NSE and MBP levels of children with severe, moderate, and mild cerebral palsy were [(21.63±1.92), (3.63±0.49) μg/L], [(17.86±1.43) μg/L, (2.21±0.07) μg/L] and [(15.14±0.95), (1.76±0.30) μg/L], respectively. After treatment, the serum NSE and MBP levels of the conventional treatment group and the comprehensive treatment group were [(13.54±2.41), (2.07±0.85) μg/L] and [(12.09±2.37), (1.81±0.69) μg/L], respectively, and the GMFM-88 score was (116.75±27.41) points and (125.94±24.93) points. The levels of NSE and MBP in the serum of children with cerebral palsy were significantly higher than those of normal children in the control group, and their levels increased with the degree of disease, and the corresponding gross motor function scores were lower. After treatment, the GMFM-88 scale assessment scores of the two groups of children were significantly improved (t values were 310.97 and 70.86, P values were both<0.05), and serum NSE and MBP levels decreased to varying degrees compared with before treatment. The decline in the comprehensive treatment group was greater than that in the conventional treatment group. Conclusions: Serum NSE and MBP levels in children with cerebral palsy at high altitude are significantly higher than those in healthy children, and their levels are closely related to the degree of impairment and GMFM-88 scores in children with cerebral palsy. Dynamic monitoring of changes in NSE and MBP levels may be responsible for the condition and treatment effects of children with cerebral palsy judgments based.