Diurnal fluctuations in cognitive function serve as a crucial regulatory foundation for maintaining neuroprotective mechanisms and metabolic homeostasis in the brain. High-fat diet (HFD) disrupts these fluctuations, yet nutritional strategies to mitigate this effect remain poorly explored. Here, the current research demonstrated that prebiotic fructo-oligosaccharides (FOS) ameliorated diurnal cognitive deficits (assessed by Barnes maze and novel object recognition tests) and restored hippocampal diurnal oscillations of neuroplasticity genes (Bdnf, Psd95, Ngf) and neuroinflammatory markers (TNFα, IL-6, IL-1β) in HFD-induced obese mice. Furthermore, FOS reshaped gut microbiota diurnal dynamics, enhanced intestinal barrier integrity (reflected in diurnal Occludin expression), and normalized the shifted diurnal patterns of microbial metabolites, particularly short-chain fatty acids (SCFAs). Consequently, FOS reinstated diurnal cognitive plasticity accompanied by normalization of SCFAs and gut-brain axis activity, highlighting a microbiota-targeted dietary approach for diurnal disruption in metabolic disorders.