Global warming and the increasing frequency of marine heatwaves (MHWs) threaten marine ecosystems and aquaculture. For the economically important spotted seabass (L. maculatus), the neuroendocrine basis of its stage-specific thermal responses has yet to be elucidated. This study examined the transcriptomic, physiological, and behavioral adaptations to chronic heat stress in late larval and late juvenile seabass over 14 days. After thermal acclimation, larvae demonstrated a marked behavioral shift, preferring warmer waters (26–34 °C). While heat stress upregulated key thermosensory genes (e.g., trpv1, trpv4) in the brain across both stages, it induced distinct expression profiles in the skin, suggesting a developmental transition from peripheral to central dominance in thermosensation. Brain transcriptomics revealed stage-specific pathway activation: juveniles engaged in neuroactive ligand-receptor interactions and MAPK signaling, whereas larvae showed enrichment in phosphatidylinositol signaling and protein processing. Both stages showed activation of the hypothalamic-pituitary-interrenal (HPI) axis (upregulation of crh, crhr1, crhr2, pomc) and heat shock response (hsp70, hsp90), accompanied by elevated serum cortisol. Notably, energy metabolism diverged significantly: larvae maintained appetite and developed hyperglycemia, while juveniles exhibited severe feeding suppression and hypoglycemia, which was correlated with differential regulation of appetite genes (npy, orexin, cck). Our results elucidate the distinct neuroendocrine mechanisms underlying thermal acclimation in L. maculatus and provide a scientific basis for developing climate-resilient aquaculture practices for this species.