This letter proposes and experimentally demonstrates an orthogonal frequency division multiplexing wavelength division multiplexing passive optical network (OFDM-WDM-PON) system based on novel chaotic set-partitioned selective mapping (SP-SLM) scheme. With the implementation of a three-dimensional chaotic system, peak-to-average power ratio (PAPR) reduction and chaotic encryption are simultaneously realized on the process of OFDM signal modulation, so as to enhance the system performance in the presence of PAPR, bit error rate (BER), fiber nonlinear tolerance and security. The experimental results show that, when compared with original OFDM signal, the OFDM signal with SP-SLM can achieve 4 dB PAPR reduction at the complementary cumulative distribution function value of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$10^{-4}$ </tex-math></inline-formula> , as well as a 1.1 dB gain in receiver sensitivity at a BER of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$10^{-3}$ </tex-math></inline-formula> . For fiber nonlinear tolerance, the optimal launch fiber power of OFDM signal with SP-SLM is 10 dBm, which is better than 9 dBm of original OFDM signal under the same received optical power of −16 dBm. Furthermore, the key space of the proposed scheme can reach up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$10^{98}$ </tex-math></inline-formula> , which is large enough to effectively protect against illegal attackers.