We propose and demonstrate a physical layer security scheme via chaotic partial transmit sequence (PTS) technique in orthogonal frequency-division multiplexing passive optical network (OFDM-PON). A 4-D hyper chaos is employed to generate the chaotic partition information, the chaotic phase weighing factors in PTS as well as the chaotic training sequence for OFDM symbol synchronization, which provides a huge key space to enhance the physical layer confidentiality. Transmission of 8.9-Gb/s 16 quadrature amplitude modulation encrypted OFDM signals is demonstrated over 20-km standard single-mode fiber, which shows reliable robustness against exhaustive attacks. Moreover, the proposed scheme improves the OFDM transmission performance due to the effective reduction of the peak-to-average power ratio of the OFDM signals by chaotic random PTS.