This study aimed to explore the association between serum non-high-density lipoprotein cholesterol (non-HDL-C) and cognitive dysfunction risk in patients with acute ischemic stroke (AIS). This cross-sectional study enrolled 583 AIS patients. Biochemical markers and lipid profile were collected after admission. AIS patients were classified into high group (non-HDL-C ≥3.4 mM) and normal group (non-HDL-C <3.4 mM). Mini-Mental State Examination scale (MMSE), Montreal Cognitive Assessment scale (MoCA), Activities of Daily Living (ADL) scale, Neuropsychiatric Inventory (NPI), and Hamilton Depression scale 21 version (HAMD-21) were applied on the third day after admission. Compared with the control group, patients of the high group had higher body mass index and higher frequency of intracranial artery stenosis, and exhibited higher levels of non-HDL-C, total cholesterol, triglycerides, low-density lipoprotein cholesterol, homocysteine, fasting blood glucose, and glycosylated hemoglobin (HbA1c), and lower levels of high-density lipoprotein cholesterol (all P<0.05). Compared with the control group, patients of the high group had significantly lower MMSE and MoCA scores (MMSE: 26.01±4.17 vs 23.12±4.73, P<0.001; MoCA: 22.28±5.28 vs 20.25±5.87, P<0.001) and higher scores on the NPI and HAMD-21 (both P<0.001). MMSE (r=-0.306, P<0.001) and MoCA scores (r=-0.251, P<0.001) were negatively associated with non-HDL-C level. Multivariate regression analysis revealed that non-HDL-C level (OR=1.361, 95%CI: 1.059-1.729, P=0.016) was independently associated with the presence of cognitive dysfunction after adjusting for confounding factors. High serum non-HDL-C level might significantly increase the risk of cognitive dysfunction after AIS.