To solve the problem of robustness of encrypted medical image watermarking algorithms, a zero watermarking algorithm based on the discrete cosine transform (DCT) and an improved DarkNet53 convolutional neural network is proposed. The algorithm targets medical images in the encrypted domain. In this algorithm, DCT is performed on the encrypted medical image to extract 32-bit features as feature 1. DarkNet53, a pre-trained network, was chosen for migration learning for the network model. The network uses a fully connected layer and a regression layer instead of the original Softmax layer and classification layer, changing the original classification network into a regression network with an output of 128. With these transformations, 128-bit features can be extracted from encrypted medical images by this network, and then DCT is performed to extract 32-bit features as feature 2. The fusion of features 1 and 2 can effectively improve the robustness of the algorithm. The experimental results show that the algorithm can accurately distinguish different encrypted medical images and can effectively restore the original information from the encrypted watermarked information under traditional and geometric attacks. Compared with other algorithms, the proposed method demonstrates better robustness and invisibility.