The two-dimensional van der Waals ferromagnetic semiconductor CrSiTe3 has attracted growing interest as an intrinsic topological magnet. Both superconductivity and enhancement of ferromagnetism, usually competing for orders, have been observed in CrSiTe3 at high pressure. However, the high-pressure structure of CrSiTe3 is still unclear, setting obstacles in understanding pressure-induced novel physics. Here, combining the Raman spectra and first-principles calculations, the structure of CrSiTe3 at high pressure has been clarified. The interlayer breathing mode located at ∼42.1 cm-1 has been observed for the first time in CrSiTe3 by ultralow-frequency Raman spectroscopy at high pressure. Theoretical calculations confirm a phase transition from the R3̅ phase to the R3 phase accompanying noticeable enhancement of the Curie temperature. Our results highlight ultralow-frequency Raman spectroscopy combined with high pressure for detecting and modulating the structure and interlayer coupling of two-dimensional materials.