The intima media thickness (IMT) of the common carotid artery (CCA) can be used to predict the risk of atherosclerosis. Many image segmentation techniques have been used for IMT measurement. However, severe noise in the ultrasound image can lead to erroneous segmentation results. To improve the robustness to noise, a fully automatic method, based on an improved Otsu’s method and an adaptive wind-driven optimization technique, is proposed for estimating the IMT (denoted as “improved Otsu-AWDO”). First, an advanced despeckling filter, i.e., “ Nagare’s filter” is used to address the speckle noise in the carotid ultrasound images. Next, an improved fuzzy contrast method (IFC) is used to enhance the region of the intima media complex (IMC) in the blurred filtered images. Then, a new method is used for automatic extraction of the region of interest (ROI). Finally, the lumen intima interface and media adventitia interface are segmented from the IMC using improved Otsu-AWDO. Then, 156 B-mode longitudinal carotid ultrasound images of six different datasets are used to evaluate the performance of the automatic measurements. The results indicate that the absolute error of proposed method is only 10.1 ± 9.6 (mean ± std in μm). Moreover, the proposed method has a correlation coefficient as high as 0.9922, and a bias as low as 0.0007. From comparison with previous methods, we can conclude that the proposed method has strong robustness and can provide accurate IMT estimations.