Atomic scale engineering of two-dimensional materials could create devices with rich physical and chemical properties. External periodic potentials can enable the manipulation of the electronic band structures of materials. A prototypical system is 3x3-silicene/Ag(111), which has substrate-induced periodic modulations. Recent angle-resolved photoemission spectroscopy measurements revealed six Dirac cone pairs at the Brillouin zone boundary of Ag(111), but their origin remains unclear [Proc. Natl. Acad. Sci. USA 113, 14656 (2016)]. We used linear dichroism angle-resolved photoemission spectroscopy, the tight-binding model, and first-principles calculations to reveal that these Dirac cones mainly derive from the original cones at the K (K) points of free-standing silicene. The Dirac cones of free-standing silicene are split by external periodic potentials that originate from the substrate-overlayer interaction. Our results not only confirm the origin of the Dirac cones in the 3x3-silicene/Ag(111) system, but also provide a powerful route to manipulate the electronic structures of two-dimensional materials.