The invisible remote photoplethysmography (rPPG) signals in facial videos can reveal the cardiac rhythm and physiological status. Recent studies show that rPPG is a non-contact way for emotion recognition disease detection and biometric identification which means there is a potential privacy problem about physiological information leakage from facial videos. Therefore it is essential to process facial videos to prevent rPPG extraction in privacy-sensitive situations such as online video meetings. In this letter we propose Privacy-Phys a novel method based on a pre-trained 3D convolutional neural network to modify rPPG in facial videos for privacy protection. Our experimental results show that our approach can modify rPPG signals in facial videos more effectively and efficiently than the previous baseline. Our method can be applied to process facial videos in online video meetings or video-sharing platforms to prevent rPPG from being captured maliciously.