Background: Many studies have shown that the levels of homocysteine (Hcy), vitamin B12 (Vit B12), and folate (FA) are abnormal in patients with Parkinson’s disease (PD), but the results have not been consistent. Therefore, we conducted this meta-analysis to summarize the features of Hcy, Vit B12, and FA in PD patients. Methods: A systematic literature search was conducted on PubMed, Cochrane Library, Web of Science, and Embase databases. Results: A total of 71 studies were included. The analysis showed the following. (1) PD patients had significantly increased Hcy level (standardized mean difference [SMD] 0.80, 95% confidence interval [CI] [0.61, 0.99]; p 0.001), and decreased Vit B12 (SMD –0.33, 95% CI [–0.43, –0.22]; p 0.001) and FA levels (SMD –0.13, 95% CI [–0.19, –0.06]; p 0.001) compared to healthy controls. (2) Higher Hcy level (SMD 0.48, 95% CI [0.30, 0.67]; p 0.001) was found in Dopaminergic medications treated PD patients than in untreated patients. (3) PD patients with cognitive impairment had higher Hcy level (SMD 0.71, 95% CI [0.50, 0.92]; p 0.001) and lower Vit B12 (SMD –0.22, 95% CI [–0.34, –0.09]; p = 0.001) and FA levels (SMD –0.17, 95% CI [–0.29, –0.04]; p = 0.009) than those with no cognitive impairment. (4) PD patients with neuropathy had significantly increased Hcy level (SMD 0.87, 95% CI [0.43, 1.31]; p 0.001) and decreased Vit B12 level (SMD –0.40, 95% CI [–0.81, –0.00]; p = 0.049) compared to PD patients with no neuropathy. Conclusions: In conclusion, PD patients may have higher Hcy levels and lower Vit B12 and FA levels than the healthy population. Thus, Hcy, Vit B12, and FA may play a role in cognitive impairment and neuropathy in PD patients.