We propose a novel security enhancement technique for a physical layer secure orthogonal frequency division multiplexed passive optical network (OFDM-PON) based on three-dimensional Brownian motion and chaos in cell (3DBCC). This method confuses an OFDM symbol via transforming it into a 3D symbol matrix and a 3D cell matrix with different size lengths. Different dividing-confusion rules then generate different complementary cumulative distribution functions (CCDFs) of peak-to-average power ratio (PAPR). And we can pre-estimate bit error rate (BER) performance by calculating the CCDF values. We also find that the processing time decreases with the matrix's side length decreasing simultaneously. A new weighted comprehensive value (Qw) is further used to evaluate the overall performance between the processing time and the BER. Finally, an experiment successfully demonstrates a physical layer secure OFDM signal transmission with 22.06-Gb/s data rate over a 25.4-km standard single mode fiber (SSMF). These results indicate that cell (53) has the weighted optimum overall performance, which verifies that the proposed encryption technique is promising for building a physical layer security enhanced OFDM-PON system with a low processing time delay and a good BER for future access network systems.