Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive behavioral and cognitive impairments. Despite growing evidence of the neuroprotective action of omega-3 polyunsaturated fatty acids (PUFAs), the effects and mechanism of omega-3 PUFAs on AD control are yet to be clarified. By crossing male heterozygous fat-1 mice with female APP/PS1 mice, we assessed whether elevated tissue omega-3 PUFA levels could alleviate AD progression and their underlying mechanism among the offspring WT, APP/PS1 and APP/PS1 × fat-1 groups at various stages. We found that the fat-1 transgene significantly increased brain omega-3 PUFA and docosahexaenoic acid (DHA) levels, and cognitive deficits together with brain Aβ-40 and Aβ-42 levels in 6-month-old APP/PS1 × fat-1 mice were significantly lower than those in APP/PS1 mice. Subsequently, the tandem mass tag (TMT) method revealed the elevated expression of cortex and hippocampus myelin-associated glycoprotein (MAG) in APP/PS1 × fat-1 mice at 2-6 months. Furthermore, GO and KEGG pathway enrichment analysis suggested that the MAG-related myelin sheath pathway and its interaction with AD were regulated by omega-3 PUFAs. Moreover, subsequent western blot assays showed that both increased endogenous omega-3 levels and in vitro supplemented DHA up-regulated MAG expression, and the AD-protective effects of DHA on LPS-induced BV2 cells were significantly weakened when MAG was inhibited by si-RNA transfection. In summary, our study suggested that omega-3 PUFAs might protect against AD by up-regulating MAG expression.