Structural magnetic resonance imaging (MRI) studies have demonstrated that the brain undergoes age-related neuroanatomical changes not only regionally but also on the network level during the normal development and aging process. In recent years, many studies have focused on estimating age using structural MRI measurements. However, the age prediction effects on different structural networks remain unclear. In this study, we established age prediction models based on common structural networks using convolutional neural networks (CNN) with data from 1,454 healthy subjects aged 18–90 years. First, based on the reference map of CorticalParcellation_Yeo2011, we obtained structural network images for each subject, including images of the following: the frontoparietal network (FPN), the dorsal attention network (DAN), the default mode network (DMN), the somatomotor network (SMN), the ventral attention network (VAN), the visual network (VN), and the limbic network (LN). Then, we built a 3D CNN model for each structural network using a large training dataset (n = 1,303) and the predicted ages of the subjects in the test dataset (n = 151). Finally, we estimated the age prediction performance of CNN compared with Gaussian process regression (GPR) and relevance vector regression (RVR). The results of CNN showed that the FPN, DAN, and DMN exhibited the optimal age prediction accuracies with mean absolute errors (MAEs) of 5.55 years, 5.77 years, and 6.07 years, respectively, and the other four networks, i.e., the SMN, VAN, VN, and LN, tended to have larger MAEs of more than 8 years. With respect to GPR and RVR, the top three prediction accuracies were still from the FPN, DAN, and DMN; moreover, CNN made more precise predictions than GPR and RVR for these three networks. Our findings suggested that CNN has the optimal age prediction performance, and our age prediction model can be potentially used for brain disorder diagnosis according to age prediction differences.