Autophagy directly regulates the amyloid beta-peptide (Aβ) clearance, and its dysfunction occurs in the early pathogenesis of Alzheimer’s disease (AD). We previously reported that docosahexaenoic acid-acylated astaxanthin monoester (AST-DHA) showed neuroprotection against AD pathology. However, its in-depth mechanism and autophagic responses in AD brains are poorly understood. Herein, SH-SY5Y cells overexpressing the Swedish mutation (K595N/M596L) of APP gene were established to preliminarily evaluate the actions of AST-DHA on reducing Aβ1-42 levels and regulating autophagy. In microglial BV2 cells, AST-DHA and free astaxanthin (F-AST) recovered p62 and LC3Ⅱ/Ⅰ levels, and restored autophagy flux by rescuing the late phase of microglial autophagy. Notably, autophagic inhibitor bafilomycin A1 blunted the abilities of AST-DHA to reduce Aβ1-42 and fibral Aβ, suggesting that AST-DHA probably promoted Aβ clearance in a microglial autophagy-dependent manner. Further studies in APP/PS1 mice verified that dietary AST-DHA and F-AST promoted Aβ phagocytosis via microglial autophagy. Significant decreases of Iba1 and p62 were observed around Aβ plaque in the hippocampus and cortex using triple fluorescence staining. Furthermore, AST-DHA exhibited superior performance over F-AST in restoring autophagic dysfunction, ameliorating Aβ burden and cognitive deficit. Our findings suggest a possible mechanism of AST-DHA in improving AD by which it restores microglial autophagy to facilitate cerebral Aβ clearance. It supports the future application of AST-DHA as an autophagic regulator in maintaining brain function.