Lunar craters are very important for estimating the geological age of the Moon, studying the evolution of the Moon, and for landing site selection. Due to a lack of labeled samples, processing times due to high-resolution imagery, the small number of suitable detection models, and the influence of solar illumination, Crater Detection Algorithms (CDAs) based on Digital Orthophoto Maps (DOMs) have not yet been well-developed. In this paper, a large number of training data are labeled manually in the Highland and Maria regions, using the Chang’E-2 (CE-2) DOM; however, the labeled data cannot cover all kinds of crater types. To solve the problem of small crater detection, a new crater detection model (Crater R-CNN) is proposed, which can effectively extract the spatial and semantic information of craters from DOM data. As incomplete labeled samples are not conducive for model training, the Two-Teachers Self-training with Noise (TTSN) method is used to train the Crater R-CNN model, thus constructing a new model—called Crater R-CNN with TTSN—which can achieve state-of-the-art performance. To evaluate the accuracy of the model, three other detection models (Mask R-CNN, no-Mask R-CNN, and Crater R-CNN) based on semi-supervised deep learning were used to detect craters in the Highland and Maria regions. The results indicate that Crater R-CNN with TTSN achieved the highest precision (of 91.4% and 88.5%, respectively) in the Highland and Maria regions, even obtaining the highest recall and F1 score. Compared with Mask R-CNN, no-Mask R-CNN, and Crater R-CNN, Crater R-CNN with TTSN had strong robustness and better generalization ability for crater detection within 1 km in different terrains, making it possible to detect small craters with high accuracy when using DOM data.