<p>Peach (<i>Prunus persica</i> L. Batsch) is among the most economically important fruit tree crops. Carotenoids in peach fruit have been intensively studied because of their relationship with fruit color and nutritional value. High carotenoid accumulation is generally a desirable trait in fruits and is associated with their aggregation in plastids. However, the understanding of the functions of carotenoid aggregates is still limited, especially with respect to their effects on chromoplast differentiation. The present study revealed that carotenoid aggregates have significant biological effects on peach. Lycopene and β-carotene aggregates promoted chlorophyll degradation and thylakoid membrane remodeling, leading to the differentiation of chloroplasts into chromoplasts in peach fruit and callus. However, the phytoene and phytofluene did not produce this effect in peach fruit. Interestingly, during lycopene and β-carotene aggregation, the stay-green-like (<i>SGRL</i>) gene was significantly activated, and further confirmed that it was an important factor affecting peach chlorophyll degradation and carotenoid accumulation. Furthermore, molecular dynamics analysis confirmed that lycopene and β-carotene had a greater effect on membrane thickness and rigidity than phytoene. This study contributes to a deeper understanding of peach carotenoid aggregates and their biological effects, confirming the effectiveness of the transgenic peach callus system.</p>