As the demand for high data volumes keeps increasing in optical access networks, transmission capacities and distance are becoming bottlenecks for passive optical networks (PONs). To solve this problem, a novel scheme based on multi-twin single sideband (SSB) modulation with direct detection is proposed and investigated in this paper. At the central office, two SSB signals are generated simultaneously with the same digital-to-analog converters (DACs). The twin-SSB signal is not only robust against frequency selected power fading introduced by chromatic dispersion (CD), but also improves the spectral efficiency (SE). By combining a twin-SSB technique with multi-band carrier-less amplitude/phase modulation (multi-CAP), different optical network units (ONUs) can be supported by flexible multi-band allocation based on software-reconfigurable optical transceivers. The Kramers–Kronig (KK) scheme is adopted on the ONU side to effectively mitigate the signal–signal beat interference (SSBI) induced by the square-law detection. The proposed system is extensively studied and validated with four sub-bands using 50 Gbps 16 quadrature amplitude modulation (QAM) modulation for each sub-band using numerical simulations. Digital pre-equalization is introduced at the transmitter-side to balance the performance of different ONUs. After system optimization, a bit error rate (BER) threshold for hard decision forward error correction (HD-FEC) code with 7% redundancy ratio (BER = 3.8 × 10−3) can be reached for all ONUs over 50-km standard single-mode fiber.