Abstract Background Motion artifacts affect the images of coronary calcified plaques. This study utilized convolutional neural networks (CNNs) to classify the motion-contaminated images of moving coronary calcified plaques and to determine the influential factors for the classification performance. Methods Two artificial coronary arteries containing four artificial plaques of different densities were placed on a robotic arm in an anthropomorphic thorax phantom. Each artery moved linearly at velocities ranging from 0 to 60 mm/s. CT examinations were performed with four state-of-the-art CT systems. All images were reconstructed with filtered back projection and at least three levels of iterative reconstruction. Each examination was performed at 100%, 80% and 40% radiation dose. Three deep CNN architectures were used for training the classification models. A five-fold cross-validation procedure was applied to validate the models. Results The accuracy of the CNN classification was 90.2 ± 3.1%, 90.6 ± 3.5%, and 90.1 ± 3.2% for the artificial plaques using Inception v3, ResNet101 and DenseNet201 CNN architectures, respectively. In the multivariate analysis, higher density and increasing velocity were significantly associated with higher classification accuracy (all P < 0.001). The classification accuracy in all three CNN architectures was not affected by CT system, radiation dose or image reconstruction method (all P > 0.05). Conclusions The CNN achieved a high accuracy of 90% when classifying the motion-contaminated images into the actual category, regardless of different vendors, velocities, radiation doses, and reconstruction algorithms, which indicates the potential value of using a CNN to correct calcium scores.