Thyroid cancer (TC) is a familiar cancer, which accounts for approximately 1% of the malignant tumors of all cancers worldwide. Recently, icariin (ICA) has been reported to play an anti-tumor role in different cancers. The study aimed to investigate the effect of ICA on TC cells to uncover the regulatory mechanism. The different concentrations of ICA were stimulated SW579 and TPC1 cells, and cell viability, apoptosis, migration, invasion and main factors of these processes were detected by CCK-8, flow cytometry, Transwell and western blot. The expression of miR-625-3p in TC tissues or in ICA-treated cells was examined by qRT-PCR. MiR-625-3p mimic and the negative control were transfected into SW579 and TPC1 cells to investigate the effect of miR-625-3p on TC. Finally, the signaling pathways of PI3K/AKT and MEK/ERK were examined by western blot. ICA significantly suppressed cell viability in a dose-dependent manner and induced apoptosis by regulating Bcl-2, Bax and cleaced-Caspase-3/-9 expression in SW579 and TPC1 cells (p < 0.001). Moreover, ICA inhibited cell migration and invasion by down-regulating MMP-9 and Vimentin in SW579 and TPC1 cells (p < 0.01 or p < 0.001). The expression level of miR-625-3p was decreased by ICA, and miR-625-3p overexpression reversed the anti-tumor effect of ICA on SW579 and TPC1 cells (p < 0.05, p < 0.01 or p < 0.001). Furthermore, ICA inactivated PI3K/AKT and MEK/ERK signaling pathways by mediating miR-625-3p in SW579 and TPC1 cells. ICA exerted antitumor effect by inhibiting cell proliferation, migration and invasion by down-regulating miR-625-3p in TC cells.