Our aim is to introduce an atherosclerotic rabbit model for inducing atherosclerosis lesions in rabbits, and to validate the model in vivo with 3T high resolution magnetic resonance imaging of the thrombosis followed a pharmacologically triggered plaque disruption. Twenty male New Zealand White rabbits were randomly allocated into an experimental group (n = 16) and a control group (n = 4). The aortic wall injuries were induced by an intravascular balloon in the experimental group rabbits after feeding them with a high cholesterol diet for 2 weeks. The pharmacological triggering with Russell’s viper venom and histamine was performed after totally 16 weeks of intermittent cholesterol feeding. All of the animals underwent both the pre-trigger and post-trigger MR examinations including TOF, T1WI, T2WI and post contrast T1WI. Euthanasia was performed in all rabbits; gross anatomy and histological specimen of aorta were obtained. MR images were analyzed and compared with histological results. Compared with the control group rabbits, the aorta of the experimental group rabbits in the pre-triggered MR images showed an increased vessel wall thickening, luminal narrowing, and vessel wall enhancement. Fourteen rabbits survived the triggering, and 8 of them developed thrombosis (58.1%). No thrombus was found in the control group. The accuracy of the multi-sequences MR including TOF, T1WI, T2WI and post contrast T1WI was 87.1% (27/31) for detecting thrombus. MR data significantly correlated with the histopathology data for both thrombus length (r = 0.94, P < 0.01) and thrombus location (r = 0.85, P < 0.01), respectively. The study demonstrated that MR reliably determined the plaque disruption and thrombus formation in the atherosclerotic rabbit model.