Three-dimensional convolutional neural networks (3DCNNs), a rapidly evolving modality of deep learning, has gained popularity in many fields. For oral cancers, CT images are traditionally processed using two-dimensional input, without considering information between lesion slices. In this paper, we established a 3DCNNs-based image processing algorithm for the early diagnosis of oral cancers, which was compared with a 2DCNNs-based algorithm. The 3D and 2D CNNs were constructed using the same hierarchical structure to profile oral tumors as benign or malignant. Our results showed that 3DCNNs with dynamic characteristics of the enhancement rate image performed better than 2DCNNS with single enhancement sequence for the discrimination of oral cancer lesions. Our data indicate that spatial features and spatial dynamics extracted from 3DCNNs may inform future design of CT-assisted diagnosis system.