Six rare guaiane-type sesquiterpene dimers xylopins A–F, having three different connecting modes through two direct C–C bonds, were isolated from the roots of Xylopia vielana. Their absolute configurations were established by NOESY analysis, Cu Kα X-ray crystallography, and experimental and calculated electronic circular dichroism spectra. Flow cytometry demonstrated the fact that compound 6 arrested the cell cycle at G2 phase and concentration-dependently induced apoptosis of DU145 cells. Furthermore, the EPT2-TGC cell model, zebrafish study and western blot analysis illustrated compound 6 could induce apoptosis by efficiently inhibiting the Wnt/β-catenin signaling pathway via decreasing the expression of β-catenin.