In semi-supervised domain adaptation (SSDA), a few labeled target samples of each class help the model to transfer knowledge representation from the fully labeled source domain to the target domain. Many existing methods ignore the benefits of making full use of the labeled target samples from multi-level. To make better use of this additional data, we propose a novel Prototype-based Multi-level Learning (ProML) framework to better tap the potential of labeled target samples. To achieve intra-domain adaptation, we first introduce a pseudo-label aggregation based on the intra-domain optimal transport to help the model align the feature distribution of unlabeled target samples and the prototype. At the inter-domain level, we propose a cross-domain alignment loss to help the model use the target prototype for cross-domain knowledge transfer. We further propose a dual consistency based on prototype similarity and linear classifier to promote discriminative learning of compact target feature representation at the batch level. Extensive experiments on three datasets, including DomainNet, VisDA2017, and Office-Home, demonstrate that our proposed method achieves state-of-the-art performance in SSDA. Our code is available at https://github.com/bupt-ai-cz/ProML.