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Objective: The main objective of this study is to evaluate the effects of integrated Chinese and Western medicine in the treatment of neurological autoimmune diseases. Materials and Methods: The literature was comprehensively searched to collect the randomized controlled trials about integrated Chinese and Western medicine in the treatment of neurological autoimmune diseases. Neurological autoimmune diseases mainly occur in the central nervous system (CNS) and peripheral nervous system. Therefore, multiple sclerosis (MS) was chosen as the representative in the CNS, and Guillain–Barre syndrome (GBS) was chosen as the representative in the peripheral nervous system. Extended Disability Status Scale (EDSS) score, effective rate, clinical symptom score, neurological functional sign score, recurrence frequency, and incidence rate of adverse reactions were chosen as the markers of outcome variables of MS, and the effective rate and Hughes score were also chosen as the markers of outcome variables of GBS. Results: For MS, the results showed that there was a significant difference in statistical analysis between the experimental group and the control group in EDSS score, the effective rate, and the recurrence frequency. However, through the comparison of clinical symptom score, neurological functional sign score, and incidence rate of adverse reaction of both two groups, the results showed that there was no significant difference in the statistical analysis. For GBS, through the comparison of effective rate and Hughes score of both two groups, the results showed that there was a significant difference in statistical analysis. Conclusions: The study demonstrated that compared with Western medicine, the therapy of integrated Chinese and Western medicine was more effective in treating neurological autoimmune diseases.