A secure transmission scheme of a W-band millimeter-wave radio-over-fiber (RoF) system based on cellular neural network (CNN) and dynamic resource allocation is proposed, in which 7-D CNN chaotic system is composed to heighten the anti-deciphering ability of a secure system, and the spectrum resources are optimized by dynamic allocation. The analyses show that the key space of our scheme can reach approximately 10112. The encrypted W-band millimeter-wave signal is successfully transmitted in the filter-OFDM RoF system of 50-km SSMF and 5 m wireless channel, and the experimental results illustrate that our proposed scheme can enhance the bit error ratio performance by approximately 0.3 dB compared with the traditional one.