Background Several studies have been performed to assess the relationship between hyperhomocysteinemia and type 2 diabetes mellitus (T2DM). However, inconsistent results have been obtained. Therefore, we performed this meta-analysis to address this knowledge gap. Methods We searched PubMed, Cochrane library, and EMBASE database for studies that evaluated the relationship between blood homocysteine (HCY) level and T2DM from inception to Jun 2019. The quality of all included studies was assessed by the Newcastle Ottawa Scale (NOS) and the Agency for Healthcare Research Quality (AHRQ). RevMan5.3 and Stata12.0 were used for data analyses. Results Twenty-five studies (including 1881 cases and 2868 controls) on blood HCY level in T2DM were pooled in our meta-analysis. The blood HCY level in the T2DM patients was significantly higher than in the healthy individuals (SMD = 0.63, 95% CI = 0.43-0.84, and p < 0.001, I-2 = 89%, p < 0.001), ignores the effects of age, sex, cardiovascular and cerebrovascular disease conditions, and other comorbidity. Additionally, in T2DM patients with nephropathy or retinopathy, blood HCY level was also significantly higher than in those with only T2DM (SMD = 1.17, 95% CI = 0.76-1.58, p < 0.001; I-2 = 90%, p < 0.001 and SMD = 0.91, 95% CI = 0.39-1.44, p <0.001; I-2 = 82%, p <0.001, respectively). Conclusion Our meta-analysis revealed the HCY level in the blood of T2DM patients was significantly higher than those of the health subjects, especially in patients with diabetic nephropathy (DN) and diabetic retinopathy (DR).