The invention discloses an ultra-wideband communication system on the basis of sub-carrier coding and a communication method thereof. The system comprises an orthogonal frequency division multiplexing ultra-wideband module, a spectrum template matching module capable of generating basic coding strategy files, a detecting and avoiding module capable of detecting channel occupation situations and a coding module, wherein coding algorithms aiming at three characteristic sub carriers are prearranged in the coding module or can be downloaded through files, the coding algorithms code sub-carrier information sequences, pilot frequency and conservation sequence data which are input according to received complete coding strategies, and then the sub-carrier information sequence, the pilot frequency and the conservation sequence data are output to the orthogonal frequency division multiplexing ultra-wideband module to be transmitted. The ultra-wideband communication system integrates multiple coding algorithms and changes the working frequency band of a sending set flexibly through a software allocation mode, the ultra-wideband communication system can accord with UWB spectrum templates of various countries, spectrum grooves of specific positions can be generated aiming at interference to avoid mutual interference effectively.