Strong interactions between different degrees of freedom lead to exotic phases of matter with complex order parameters and emergent collective excitations. Conventional techniques, such as scattering and transport, probe the amplitudes of these excitations, but they are typically insensitive to phase. Therefore, novel methods with phase sensitivity are required to understand ground states with phase modulations and interactions that couple to the phase of collective modes. Here, by performing phase-resolved coherent phonon spectroscopy (CPS), we reveal a hidden spin–lattice coupling in a vdW antiferromagnet FePS ₃ that eluded other phase-insensitive conventional probes, such as Raman and X-ray scattering. With comparative analysis and analytical calculations, we directly show that the magnetic order in FePS ₃ selectively couples to the trigonal distortions through partially filled t _{2 g} orbitals. This magnetoelastic coupling is linear in magnetic order and lattice parameters, rendering these distortions inaccessible to inelastic scattering techniques. Our results not only capture the elusive spin–lattice coupling in FePS ₃ but also establish phase-resolved CPS as a tool to investigate hidden interactions.