Pear fruit typically contains abundant highly lignified cells, known as stone cells, which have a negative impact on the fruit's edibility and processing quality. Despite extensive physiological and molecular research, there remains a limited understanding of the precise spatiotemporal aspects of lignification in flesh cells during pear development, particularly regarding the initiation of lignification and expansion of stone cell clusters. Here, an emerging bioorthogonal chemistry-based imaging technique was employed to in vivo visualize cell lignification dynamics in developing pear fruit. Specific identification of active sites undergoing lignification revealed that initial lignification of flesh cells occurred at 10 days after full bloom (DAFB), resulting in the formation of primordial stone cells (PSCs). These PSCs exhibited a random distribution and showed significantly larger diameter and area compared to normal parenchyma cells. Subsequently, PSCs developed pit canals and initiated lignification process in their neighboring cells at 15 DAFB. A cascading effect in the formation of stone cell aggregations was visualized by tracing of the lignification trajectory. This expansion process exhibited a domino effect, whereby lignification progressively spread from one cell to the next, creating a cascading pattern of stone cell formation. Finally, a cellular developmental model was proposed for stone cell formation. This study presented a procedure for applying the cutting-edge technology, click chemistry imaging, to get insights into practical scientific questions. The findings elucidated the spatiotemporal dynamics of active lignification sites in pear fruit at the cellular level, thereby enhancing our understanding of the initiation and aggregation processes in stone cell formation.