Orthogonal frequency-division multiplexing (OFDM) passive optical network (PON) has been considered to be a promising next-generation broadband wired access solution. However, based on the current tree-based architecture, existing OFDM PON systems face severe challenges when increasing the scalability and data-rate performance. In this paper, we propose a high-performance virtual-tree orthogonal frequency-division multiple access PON system (VTOPS). With the virtual-tree architecture and coupled with the use of inexpensive direct modulation, VTOPS features high reliability, scalability, spectrum efficiency, and cost effectiveness all at once. For governing the flexible/fair access and dynamic allocation of bandwidth, VTOPS incorporates a rate-based medium access control (MAC) scheme. The MAC scheme performs dynamic rate adjustment using a neural-fuzzy system. By adjusting the system parameters, the MAC scheme can achieve a wide range of delay and fairness performance under a variety of traffic patterns. Finally, we show both theoretical and experimental results to demonstrate that, by applying the power pre-emphasis algorithm and adaptive subchannel modulation, VTOPS achieves 40 Gb/s downlink and 40 Gb/s uplink transmissions, using low-cost 10 GHz directly modulated lasers.