Plenty of rural populations still chronically exposed to indoor coal burning, which tremendously raises the risk of cardiovascular disease, in China. This study aimed to further investigate the association between indoor coal burning exposure and atherosclerotic cardiovascular diseases to search for relevant markers for disease prevention. Herein, we conducted a cross-sectional study, carried out on 752 local long-term residents with or without bituminous coal for cooking and heating indoor, in Nangong County, Hebei Province, China. We utilized a nearest neighbor propensity score match (PSM) with a caliper distance equal to 0.001 to eliminate bias caused by confounding factors. The expression of genes associated with endothelial activation (CCL2, CCL5, CXCL8, CXCL12, VCAM, ICAM, SELP) in primary human coronary artery endothelial cells (HCAECs) were quantified through ex vivo biosensor assay. Multiple linear regression models with stratification analyses by gender and binary logit regression models were used to evaluate the association between mRNA expression of biosensor genes and indoor coal burning pollution or carotid atherosclerosis, respectively. Protein secretion level was detected by enzyme-linked immunosorbent assay (ELISA). The prevalence of carotid atherosclerosis in exposure group was higher than control (P = 0.023), before PSM. The gene expression of CCL2 in exposure group was significantly higher than control (P = 0.002). Indoor coal burning exposure was correlated with gene expression of CCL2 (β = 3.45, 95 % CI: 0.04–6.87, P = 0.047) and CXCL8 (β = 1.25, 95 % CI: 0.02–2.49, P = 0.046) in female. A higher risk of carotid atherosclerosis was observed in the same as the increase expression of CCL2 (OR = 1.07, 95 % CI: 1.01–1.14, P = 0.020). In conclusion, prolonged exposure to indoor coal burning could elevate the gene expression of CCL2 by activating vascular endothelial cells and was relative to the initiation of carotid atherosclerosis.