We study the performance of an orthogonal modulation system with frequency-shift keying (FSK) label and optical Manchester-coded (MC) payload. Simulation result shows that by introducing an optical MC payload, the available extinction ratio (ER) value of a FSK and intensity modulation (IM) orthogonal modulation system can be improved from 5 to 9 dB for system optimization, exhibiting great advantages over the traditional non-return-to-zero (NRZ) payload. Besides, the bit error rate (BER) characteristics of both label and payload show a more remarkable advantage than that of NRZ coding, verifying itself as a perfect candidate for the payload coding method in orthogonal modulation systems.