The invention discloses a real-time acoustic fingerprinting system and method. The real-time acoustic fingerprinting system comprises a voice collecting and storing module, a phoneme detecting moduleand a speaker identification module. The voice collecting and storing module is used for collecting and storing voice data, the phoneme detecting module is used for detecting the phoneme category andthe phoneme position which exit in the voice data, and the speaker identification module is used for confirming identity information of a speaker according to the phoneme category and the phoneme position. Speakers irrelevant to a text can be identified, and the experience degree of the user is increased; and phoneme is adopted as the most basic composition unit in language, higher identifiabilityis achieved, meanwhile contents irrelevant to the text are converted into contents relevant to the text, and the difficulty of speaker identification is lowered.