Revealing the hydrogen bonding paradigm is critical to clarify the formation mechanism of hydrogen bonded materials. The nucleation process of a typical nonlinear optical crystal, KH 2 PO 4 , is identified by in situ molecular vibration spectroscopy, which effectively demonstrates the oriented role of hydrogen bonding in local structure engineering. On the basis of the vibrational evolution of hydrogen bonds, the partition of different periods in the formation of crystalline KH 2 PO 4 from aqueous solution becomes clear. In KH 2 PO 4 aqueous solution, there are hydrated status, (H 2 PO 4 − ) n aggregations, and prenucleation clusters. The prenucleation clusters exist in the solution with a metastable status over a period of time, and then they will transform into crystalline ones within a short time. Two distinct roles of P−O•••H−O−P hydrogen bonding in the formation of crystalline KH 2 PO 4 have been distinguished. At the initial stage of aggregation formation, P−O bond in H 2 PO 4 − group guides the P−O•••H−O−P hydrogen bonding, leading to the H 2 PO 4 − that retains C 2v symmetry, whereas P−O•••H−O−P hydrogen bonding guides the twist and rotation of H 2 PO 4 − groups in prenucleation clusters, promoting the local structural evolution of (H 2 PO 4 − ) n from C 2v to D 2d and the formation of crystalline KH 2 PO 4 nuclei. The present work deepens the hydrogen bonding effect that can warrant much space to adjust the chemical bonding environment in constructing crystallographic frames.