MicroRNAs (miRNAs) and aberrant glycosylation both play important roles in tumor metastasis. In this study, the role of miR-23a in N-glycosylation and the metastasis of mouse hepatocellular carcinoma (HCC) cells was investigated. The miRNA expression array profiles that were confirmed by qPCR and Western blot analyses revealed higher miR-23a expression levels in Hca-P cells (with lymphatic metastasis potential) than in Hepa1-6 cells (with no lymphatic metastasis potential), while the expression of mannoside acetylglucosaminyltransferase 3 (Mgat3) was negatively associated with metastasis potential. Mgat3 is a key glycosyltransferase in the synthesis of the bisecting (β1,4GlcNAc branching) N-glycan structure. Bioinformatics analysis indicated that Mgat3 may be a target of miR-23a, and this hypothesis was verified by dual-luciferase reporter gene assays. Furthermore, we found that the transcription factor Runx2 can directly bind to the miR-23a gene promoter and promote its expression, as shown in dual-luciferase reporter gene assays and ChIP assays. Collectively, these results indicate that miR-23a might increase the metastatic potential of mouse HCC by affecting the branch formation of N-glycan chains presented on the cell surface through the targeting of the glycosyltransferase Mgat3. These findings may provide insight into the relationship between abnormal miRNA expression and aberrant glycosylation during tumor lymphatic metastasis.