Liquid–liquid phase transition (LLPT) is a transition from one liquid state to another with the same composition but distinct structural change, which provides an opportunity to explore the relationships between structural transformation and thermodynamic/kinetic anomalies. Herein the abnormal endothermic LLPT in Pd43Ni20Cu27P10glass-forming liquid was verified and studied by flash differential scanning calorimetry (FDSC) and ab initio molecular dynamics (AIMD) simulations. The results show that the change of the atomic local structure of the atoms around the Cu-P bond leads to the change in the number of specific clusters <0 2 8 0> and <1 2 5 3>, which leads to the change in the liquid structure. Our findings reveal the structural mechanisms that induce unusual heat-trapping phenomena in liquids and advance the understanding of LLPT.