In the intricate network environment, the secure transmission of medical images faces challenges such as information leakage and malicious tampering, significantly impacting the accuracy of disease diagnoses by medical professionals. To address this problem, the authors propose a robust feature watermarking algorithm for encrypted medical images based on multi‐stage discrete wavelet transform (DWT), Daisy descriptor, and discrete cosine transform (DCT). The algorithm initially encrypts the original medical image through DWT‐DCT and Logistic mapping. Subsequently, a 3‐stage DWT transformation is applied to the encrypted medical image, with the centre point of the LL3 sub‐band within its low‐frequency component serving as the sampling point. The Daisy descriptor matrix for this point is then computed. Finally, a DCT transformation is performed on the Daisy descriptor matrix, and the low‐frequency portion is processed using the perceptual hashing algorithm to generate a 32‐bit binary feature vector for the medical image. This scheme utilises cryptographic knowledge and zero‐watermarking technique to embed watermarks without modifying medical images and can extract the watermark from test images without the original image, which meets the basic requirements of medical image watermarking. The embedding and extraction of watermarks are accomplished in a mere 0.160 and 0.411s, respectively, with minimal computational overhead. Simulation results demonstrate the robustness of the algorithm against both conventional attacks and geometric attacks, with a notable performance in resisting rotation attacks.