Several studies have reported an association between levels of folate, homocysteine, and vitamin B12 and the risk of colorectal polyps. Here, our aim is to examine the possible effect of folate, homocysteine, and vitamin B12 levels on the risk of colorectal polyps by means of meta-analysis based quantitative synthesis. According to our inclusion/exclusion criteria, a total of 13 case–control studies were enrolled. The P-value of the association test, standard mean difference (SMD), and 95% confidence interval (CI) were calculated. Pooled analysis data showed a negative correlation between the risk of colorectal polyps and the levels of serum folate, red blood cell (RBC) folate, or vitamin B12 (all P>0.05). Nevertheless, for homocysteine level, we also observed a statistically significant difference between cases and controls in the overall and subgroup analysis of hospital-based control (HB), population-based control (PB), Chinese, Caucasian, or Asian (all P<0.05, SMD > 0). We found that increased levels of homocysteine may be statistically and significantly related to the risk of colorectal polyps.