Collective excitations that involve both vibrational and magnetic characters, arising from strong coupling between the lattice and spins, are of fundamental interest in ultrafast manipulation of magnetization. Although previous experimental studies have successfully observed the spin dynamics of a coherent electromagnon that reflects this coupling, the associated atomic motions have not been directly observed. Here we use time-resolved X-ray diffraction to directly measure both the ultrafast structural motion and the associated spin dynamics following the excitation of a coherent electromagnon by an intense THz pulse in a multiferroic hexaferrite. Comparing the dynamics of the two different components, one striking outcome is the different phase shifts relative to the driving field, gives deeper insights into the excitation process of electromagnons. The observation of combined lattice and magnetization dynamics of the electromagnon resonance paves the way to access the magnetoelectric coupling strength in ultrafast timescales, which remains a missing fundamental parameter for ultrafast control of magnetism.