Species of the Magnoliaceae family are valued for their ornamental qualities and are widely used in landscaping worldwide. However, many of these species are endangered in their natural environments, often due to being overshadowed by overstory canopies. The molecular mechanisms ofMagnolia’s sensitivity to shade have remained hitherto obscure. Our study sheds light on this conundrum by identifying critical genes involved in governing the plant’s response to a light deficiency (LD) environment. In response to LD stress,Magnolia sinostellataleaves were endowed with a drastic dwindling in chlorophyll content, which was concomitant to the downregulation of the chlorophyll biosynthesis pathway and upregulation in the chlorophyll degradation pathway. TheSTAY-GREEN(MsSGR) gene was one of the most up-regulated genes, which was specifically localized in chloroplasts, and its overexpression in Arabidopsis and tobacco accelerated chlorophyll degradation. Sequence analysis of theMsSGRpromoter revealed that it contains multiple phytohormone-responsive and light-responsive cis-acting elements and was activated by LD stress. A yeast two-hybrid analysis resulted in the identification of 24 proteins that putatively interact with MsSGR, among which eight were chloroplast-localized proteins that were significantly responsive to LD. Our findings demonstrate that light deficiency increases the expression ofMsSGR, which in turn regulates chlorophyll degradation and interacts with multiple proteins to form a molecular cascade. Overall, our work has uncovered the mechanism by whichMsSGRmediates chlorophyll degradation under LD stress conditions, providing insight into the molecular interactions network of MsSGR and contributing to a theoretical framework for understanding the endangerment of wild Magnoliaceae species.