Mitochondria play a crucial role in cellular processes such as growth, differentiation, and energy conversion. Dysfunctional mitochondria have been implicated in Alzheimer's disease (AD), making mitochondrial improvement a promising therapeutic approach. SIRT3, a mitochondrial deacetylase, modulates mitochondrial function by deacetylating associated proteins. This study aimed to enhance the activity of honokiol, a natural SIRT3 modulator, and improve mitochondrial function for neuroprotective activity, using mitochondria targeting strategy. We synthesized mitochondrial targeting peptide conjugates using XJB as a carrier and found that honokiol conjugates exhibited lower toxicity and higher activity on neuronal injury models in vitro and in vivo (Zebrafish model) at lower concentrations compared to honokiol. The neuroprotective mechanism may involve the activation of cellular autophagy-related pathways, promotion of SIRT3 pathway activation, and up-regulation of mitochondrial fusion-associated protein Mfn-1 expression under damaged conditions. This study offers a promising approach for developing anti-Alzheimer's disease (AD) natural product derivatives based on SIRT3 regulation.