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The security of deep neural networks (DNNs) has attracted increasing attention due to their widespread use in various applications. Recently, the deployed DNNs have been demonstrated to be vulnerable to Trojan attacks, which manipulate model parameters with bit flips to inject a hidden behavior and activate it by a specific trigger pattern. However, all existing Trojan attacks adopt noticeable patch-based triggers (e.g., a square pattern), making them perceptible to humans and easy to be spotted by machines. In this paper, we present a novel attack, namely hardly perceptible Trojan attack (HPT). HPT crafts hardly perceptible Trojan images by utilizing the additive noise and per pixel flow field to tweak the pixel values and positions of the original images, respectively. To achieve superior attack performance, we propose to jointly optimize bit flips, additive noise, and flow field. Since the weight bits of the DNNs are binary, this problem is very hard to be solved. We handle the binary constraint with equivalent replacement and provide an effective optimization algorithm. Extensive experiments on CIFAR-10, SVHN, and ImageNet datasets show that the proposed HPT can generate hardly perceptible Trojan images, while achieving comparable or better attack performance compared to the state-of-the-art methods. The code is available at: https://github.com/jiawangbai/HPT.