Specimen mammography is one of the widely used intraoperative methods assessing margin status in breast conserving surgery. We performed a meta-analysis to evaluate the diagnostic accuracy of specimen mammography. Literature databases including Pubmed, Cochrane Library, Web of Science and EMBASE were searched prior to May 2020. 18 studies with a total of 1142 patients were included. Data was extracted to perform pooled analysis, heterogeneity testing, threshold effect testing, sensitivity analysis, publication bias analysis and subgroup analyses. The pooled weighted values were a sensitivity of 0.55 (95% CI, 0.45–0.64), a specificity of 0.85 (95% CI, 0.77–0.90), a DOR of 7 (95% CI, 4–11) and a pooled positive likelihood ratio of 3.6 (95% CI 2.4-5.3). The area under the receiver operator characteristic curve was 0.75 (95% CI 0.71-0.78). In the subgroup analysis, the pooled specificity in the positive margin defined as tumor at margin subgroup was lower than the other positive margin definition subgroup (0.79 [95% CI: 0.66, 0.91] vs. 0.88 [95% CI: 0.81, 0.95], p = 0.01). Our findings indicated specimen mammography to be an accurate and intraoperative imaging technique for margin assessment in breast conserving surgery.