We report a comprehensive Raman scattering study on layered MPS3 (M=Mn, Fe, Ni), a two-dimensional magnetic compound with weak van der Waals interlayer coupling. The observed Raman phonon modes have been well assigned by the combination of first-principles calculations and the polarization-resolved spectra. Careful symmetry analysis on the angle-dependent spectra demonstrates that the crystal symmetry is strictly described by C2h but can be simplified to D3d with good accuracy. Interestingly, the three compounds share exactly the same lattice structure but show distinct magnetic structures. This provides us with a unique opportunity to study the effect of different magnetic orders on lattice dynamics in MPS3. Our results reveal that the in-plane N(e)el antiferromagnetic (AF) order in MnPS3 favors a spin–phonon coupling compared to the in-plane zig-zag AF in NiPS3 and FePS3. We have discussed the mechanism in terms of the folding of magnetic Brillouin zones. Our results provide insights into the relation between lattice dynamics and magnetism in the layered MPX3 (M=transition metal, X=S, Se) family and shed light on the magnetism of monolayer MPX3 materials.