The crystal structure and hydrogen‐bonded chains of 1,3‐diphenylurea were found to have abrupt changes when the pressure increased to 1.8 GPa. Based on Raman spectra, the intermolecular interactions, the vibrations of chemical groups, and the molecular conformation were clearly distinguished from the initial state. The anisotropic compression of the original crystal structure and the occurrence of structural phase transition were confirmed by the results of in situ high‐pressure synchrotron X‐ray diffraction experiments. The new phase was stable up to about 10.0 GPa. The inevitable creasing of the N–H⋯O hydrogen‐bonded chains was derived from the remarkable shrink of distance between hydrogen‐bonded chains, which can be treated as the main reason leading to this phase transition. The first‐principle calculations and Hirshfeld surfaces further confirmed the analysis of the experimental results. This study demonstrates that excessively reducing the space between of hydrogen‐bonded chains will rearrange the self‐assembly of supramolecular materials.