Objective: The objective of this study is to develop a deep-learning based detection and diagnosis technique for carotid atherosclerosis using a portable freehand 3D ultrasound (US) imaging system. Methods: A total of 127 3D carotid artery datasets were acquired using a portable 3D US imaging system. A U-Net segmentation network was firstly applied to extract the carotid artery on 2D transverse frame, then a novel 3D reconstruction algorithm using fast dot projection (FDP) method with position regularization was proposed to reconstruct the carotid artery volume. Furthermore, a convolutional neural network was used to classify the healthy case and diseased case qualitatively. 3D volume analysis including longitudinal reprojection algorithm and stenosis grade measurement algorithm was developed to obtain the clinical metrics quantitatively. Results: The proposed system achieved sensitivity of 0.714, specificity of 0.851 and accuracy of 0.803 respectively in diagnosis of carotid atherosclerosis. The automatically measured stenosis grade illustrated good correlation (r=0.762) with the experienced expert measurement. Conclusion: the developed technique based on 3D US imaging can be applied to the automatic diagnosis of carotid atherosclerosis. Significance: The proposed deep-learning based technique was specially designed for a portable 3D freehand US system, which can provide carotid atherosclerosis examination more conveniently and decrease the dependence on clinician's experience.