As an essential component of Internet of Things, GPS-enabled devices record tremendous digital traces, which provide a great convenience for understanding human mobility. How to discover transportation modes efficiently from such valuable sources has come into the spotlight. In this paper, the transportation mode detection is treated as a dense classification task, and a Similarity Entropy-based Encoder-Decoder (SEED) model is proposed. We first design an encoder-decoder backbone for end-to-end mode detection. Then, a semi-supervised learning module based on similarity entropy is proposed to exploit numerous unlabeled data. Specifically, we stack several convolutional layers as an encoder to capture hierarchical features from fixed-length trajectories, and then adopt transposed convolutional layers as a decoder. For a semi-supervised module, inspired by entropy regularization, we use the K-Means algorithm to cluster prototype vectors from the encoder’s predictions. We then fine-tune the encoder by sharpening the similarity distribution between unlabeled predictions and prototypes, aiming to make the former close to one prototype only while staying away from others. A majority-voting post-processing method is used to alleviate jitter impact when inferring. Experimental results show that SEED significantly outperforms segmentation-then-inference methods. Furthermore, the similarity entropy-based module can improve the generalization performance of the model, and the metrics such as intersection over union can be increased by 5% over baselines. All of these verify the superiority of our method.