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 acoding 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 frequencyand 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.