In order to guarantee the information of the W-band wireless communication system from the physical layer, this paper proposes the sliced chaotic encrypted (SCE) transmission scheme based on key masked distribution (KMD). The scheme improves the security of free space communication in the W-band millimeter-wave wireless data transmission system. In this scheme, the key information is embedded into the random position of the ciphertext information, and then the ciphertext carrying the key information is encrypted by multi-dimensional chaos. Chaotic system 1 constructs a three-dimensional discrete chaotic map for implementing KMD. Chaotic system 2 constructs complex nonlinear dynamic behavior through the coupling of two neurons, and the masking factor generated is used to realize SCE. In this paper, the transmission of 16QAM signals in a 4.5 m W-band millimeter-wave wireless communication system with a rate of 40 Gb/s is proved by experiments, and the performance of the system is analyzed. When the input optical power is 5 dBm, the bit error rate (BER) of the legitimate encrypted receiver is 1.23 × 10−3. When the offset of chaotic sequence x and chaotic sequence y is 100, their BERs are more than 0.21. The key space of the chaotic system reaches 10192, which can effectively prevent illegal attacks and improve the security performance of the system. The experimental results show that the scheme can effectively distribute the keys and improve the security of the system. It has great application potential in the future of W-band millimeter-wave wireless secure communication.