Objective The study was aimed to investigate the transport and deposition behaviors of low-density lipoproteins (LDL) in the carotid artery and explore their associations with hemodynamic and morphological factors, so as to provide theoretical references for assessing the risk and predisposing regions of atherosclerosis based on the characteristics and associated factors of LDL deposition at the carotid artery wall. Methods We firstly built subject-specific computational models of the carotid artery based on medical images acquired from six healthy volunteers, secondly simulated the transport and wall deposition of LDL under pulsatile flow conditions, and finally quantitatively analyzed the correlations of wall LDL concentration and the total area of regions with LDL concentration polarization with flow velocity in and morphological parameters of the carotid artery. Results Regions with significant LDL deposition often appeared in the carotid sinus near the distal end of the common carotid artery, with the degree and spatial distribution of deposition differing considerably among subjects. The degree of LDL deposition was determined mainly by flow velocity, i.e., the lower the flow velocity was, the higher the degree of LDL deposition and accordingly the larger the area of wall regions with LDL concentration polarization was; whereas the spatial distribution of LDL deposition was significantly affected by the morphological characteristics (especially bifurcation eccentricity ratio) of the carotid artery, for example, the distribution patterns could be divided into two typical types (i.e., circular distribution, unilateral distribution) according to the value of bifurcation eccentricity ratio. Conclusions Flow velocity and morphological characteristics of the carotid artery are major factors determining respectively the degree and spatial distribution of LDL deposition, and therefore subject-specifically measuring these parameters would provide useful information for screening individuals at high risk of atherosclerosis or identifying atheroprone regions.