In this paper, the high-security three-dimensional (3D) carrier-less amplitude-phase (CAP) modulation based on 3D space constellation masking in multi-core fiber (MCF) transmission is proposed. Logistic Map model and Four-wing hyper-chaotic systems are employed to implement bit-level encryption, displacement masking, and space masking. This way, we achieved a key space of 1 × 1083 size, which resists violent attacks, and improves the physical layer security of the system. The superposition combined two chaotic models reduces the difficulty of implementation and enables more security for constellation encryption. A 280 Gb/s encrypted 3D-CAP32 signal transmission over 2.5 km MCF is experimentally demonstrated. The experimental results show that the proposed scheme can effectively resist illegal attack from an un-authorized optical network unit (ONU), and compared with an unencrypted 3D-CAP32 signal, the encrypted 3D-CAP32 signal has a receiver sensitivity penalty of 0.38 dB in a back-to-back configuration at a BER of 1 × 10−3. It is a strong candidate for the future highly-secured optical access network.