Chronic cerebral hypoperfusion (CCH) results in cognitive impairment, with mitochondrial dysfunction identified as a key contributor. The opening of the mitochondrial permeability transition pore (mPTP) is closely associated with mitochondrial dysfunction and excessive mitophagy, particularly under stress conditions. Dl-3-n-Butylphthalide (Dl-NBP) has been shown to ameliorate cognitive impairment caused by CCH. However, whether Dl-NBP exerts its effects by inhibiting mPTP opening and mitigating excessive mitophagy remains unclear. In this study, we established a rat model of CCH through permanent bilateral common carotid artery occlusion (BCCAO) and explored the neuroprotective effects of Dl-NBP and its underlying mechanisms. The neuroprotective effects of Dl-NBP were evaluated using the Morris water maze test, and protein expression levels related to mPTP, apoptosis, and mitophagy were assessed through Western blotting and immunofluorescence. The ultrastructural changes in mitochondrial morphology and mitophagosomes were observed using transmission electron microscopy. We found that CCH led to cognitive impairment in rats, along with increased expression of p53, cytochrome-c, cleaved-Caspase3, LC3II/LC3I, Beclin1, P62, PINK1, and Parkin in the hippocampal tissue. Additionally, CCH caused an accumulation of mitophagosomes in the hippocampal tissue, although it did not affect Cyclophilin D (CypD) expression levels. However, Dl-NBP reversed these changes, except for CypD. Taken together, these findings suggest that Dl-NBP may improve cognitive impairment in CCH rats, potentially through the reduction of hippocampal neuron apoptosis by inhibiting mPTP opening and excessive mitophagy. Dl-NBP may represent a potential therapeutic strategy for treating cognitive impairment associated with CCH.