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Triglyceride (TG) and atherogenic index of plasma (AIP) have been acknowledged to be risk factors for vascular insults, but their impacts on the brain system remain elusive. To fill in some gaps, we investigated associations of TG and AIP with brain structure, leveraging the UK Biobank database. TG and high-density lipoprotein cholesterol (HDL-C) were examined at baseline and AIP was calculated as log (TG/HDL-C). We build several linear regression models to estimate associations of TG and AIP with volumes of brain grey matter phenotypes. Significant inverse associations of TG and AIP with volumes of specific subcortical traits were observed, among which TG and AIP were most significantly associated with caudate nucleus (TG: β [95% confidence interval CI] = −0.036 [−0.051, −0.022], AIP: −0.038 [−0.053, −0.023]), thalamus (−0.029 [−0.042, −0.017], −0.032 [−0.045, −0.019]). Higher TG and AIP were also considerably related with reduced cortical structure volumes, where two most significant associations of TG and AIP were with insula (TG: −0.035 [−0.048, −0.022], AIP: −0.038 [−0.052, −0.025]), superior temporal gyrus (−0.030 [−0.043, −0.017], −0.033 [−0.047, −0.020]). Modification effects of sex and regular physical activity on the associations were discovered as well. Our findings show adverse associations of TG and AIP with grey matter volumes, which has essential public health implications for early prevention in neurodegenerative diseases.