Longan (Dimocarpus longan Lour.) exhibits vigorous vegetative growth and strong fruit setting ability but suffers from alternate bearing. The role of endogenous hormones in mediating the effects of fruiting load remains unclear. This study investigated how the initial fruiting branch rate (IFBR) and initial fruit number per cluster (INFC) regulate endogenous hormones in the aril and leaflets of mature ‘Shixia’ longan. Key findings reveal the aril as the hormonal sink, accumulating auxin (IAA) and abscisic acid (ABA), while leaves retain IAA precursors (TRP) and conjugates. Higher IFBR and INFC increased the demand for IAA in the aril to support expansion but simultaneously elevated ABA levels in leaves. Notably, IFBR exerted a stronger influence than INFC. These hormonal changes were significantly correlated with the fruit shedding rate and soluble solid content. Overall, the endogenous hormone profile was optimized by maintaining a moderate IFBR of approximately 60% and an INFC within the range of 60 to 80, achieving balance between fruit expansion, leaf vitality, and yield. The results provide a hormonal basis for precise crop load management in longan cultivation.