In this paper, we propose and experimentally demonstrate a novel multi-band chaotic non-orthogonal matrix (CNOM)-based encryption scheme for secure orthogonal frequency division multiplexing (OFDM) passive optical networks. The dimension of non-orthogonality is exploited in the encryption with the CNOM, where both faster-than-Nyquist signaling and redundant precoding were employed to dynamically scramble the original number of subcarriers of each sub-band and fix the overall data rate. Both simulation and experimental results of a 10.6 Gb/s 4-QAM transmission over a 20-km standard single-mode fiber showed that the total key space significantly increases by 1.4×10482 and 1.72×10653 times, as the number of sub-bands increases from 1 to 10 and 15, with a considerable reduction in computational complexity of 90% and 93.33% in complex-valued multiplication, and 90.76% and 94.12% in complex-valued addition, when encrypting one OFDM symbol, respectively. Moreover, the improved resilience to the frequency roll-off has also been verified by using additional permutation matrices in the proposed encryption algorithm.