Recently the liquid–liquid transition (LLT) was found in a molecular liquid, triphenyl phosphite, which allows us to follow the kinetics of the transformation of one liquid to another. Here we investigate the microscopic structural change during the LLT by means of time-resolved synchrotron x-ray scattering measurements. We confirm that during spinodal-decomposition-type transformation a new peak corresponding to a particular intermolecular phosphor–phosphor distance emerges and grows with time. This indicates that short-range order develops in the liquid during LLT. We show that the short-range order does not represent the crystalline structure, but the locally favoured structure. We found that the temporal increase of the intensity of this peak, i.e., the fraction of locally favoured structures, is proportional to that of the heat released during the transformation. This means that the formation of locally favoured structures is the origin of the heat release. This is consistent with the proposal that the order parameter governing LLT is the number density of locally favoured structures. This yields a valuable insight into the nature of the ordering in the liquid–liquid transition.