In this paper, a high-security three-dimensional carrier-less amplitude-phase (3D-CAP) modulation is proposed, which can be used for short-distance multi-core fiber communication. Using a brand-new 3D constellation dubbed Triple-Decker, the 3D-CAP passive optical network's bit error rate (BER) performance is improved. This constellation's constellation figure of merit can be increased by changing the three-dimensional constellation distribution through geometric shaping. To provide constellation encryption for Triple-Decker by rotation, expansion, and time slot scrambling at the physical layer in 3D-CAP passive optical network (3D-CAP-PON), a four-dimensional hyperchaotic system known as Fu's model is utilized. We successfully carried out an experiment demonstrating 25.5 Gb/s 3D-CAP transmission over a 7-core fiber communication system. Experimental results illustrate that, compared to the traditional 3D constellation, our suggested scheme can obtain 0.6 dB receiving sensitivity gain at the BER∼1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−3</sup> . The achieved key space is 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">120</sup> . Due to its strong security and superior performance, this scheme has a promising future in short-distance secure communication.