Cancer metastasis has been a major impediment to effective cancer treatment and is the major cause of cancer-related death. Polyphenols compounds have been reported to possess anti-metastasis activity through their inhibitory activity of matrix metalloproteinases (MMPs). In this paper, twelve polyphenols compounds, including three novel phenols, named selaphenins A-C (1-3), two known selaginellin derivatives (4 and 5), together with seven known biflavonoids (6-12) were isolated from the plant of Selaginella tamariscina. Their structures were elucidated by extensive spectroscopic analyses. Notably, polyphenols compound 10 suppressed the migration of A549 cells by primary targeting MMP-9. The antitumor activity of compound 10 was possibly due to the induction of cell apoptosis through intrinsic apoptosis pathways, accompanied by increasing the expression of Bax and caspase-3 in a dose-dependent manner. This study provides evidence that polyphenols analogues from S. tamariscina as inhibitors of MMP-9 exhibited potential migration inhibition activities.