The manipulation of spin−phonon coupling in both formations and explorations of magnetism in two-dimensional van der Waals ferromagnetic semiconductors facilitates unprecedented prospects for spintronic devices. The interlayer engineering with spin−phonon coupling promises controllable magnetism via organic cation intercalation. Here, spectroscopic evidence reveals the intercalation effect on the intrinsic magnetic and electronic transitions in quasi-two-dimensional Cr 2 Ge 2 Te 6 using tetrabutyl ammonium (TBA + ) as the intercalant. The temperature evolution of Raman modes, E g 3 and A g 1 , along with the magnetization measurements, unambiguously captures the enhancement of the ferromagnetic Curie temperature in the intercalated heterostructure. Moreover, the E g 4 mode highlights the increased effect of spin−phonon interaction in magnetic-order-induced lattice distortion. Combined with the first-principle calculations, we observed a substantial number of electrons transferred from TBA + to Cr through the interface. The interplay between spin−phonon coupling and magnetic ordering in van der Waals magnets appeals for further understanding of the manipulation of magnetism in layered heterostructures.