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• Pyrroloquinoline quinone (PQQ) is widely used as a dietary supplement in Europe and America. • A new supramolecular extractant was designed for the separation of PQQ from fermentation broth. • The extraction driving force was inferred as an ion-pair and π-π interaction between PQQ and BC. In this paper, new supramolecular extractants, which contained surfactant, alkane and alkanol, were designed and used to separate PQQ. After a series of tests, the optimal extractant composition was determined as benzalkalonium (C 8 -C 16) chloride (BC): n -hexane: n -pentanol, and the highest extraction rate could reach 98%. The extraction equilibrium could be reached in five minutes. The mechanism of the extraction selectivity was inferred as an ion-pair and π-π complexation interaction between PQQ and BC, which was indicated by UV and fluorescence quenching experiments. To recycle the organic extractant, the extract was back-extracted with sodium chloride solution. After extraction, back extraction and crystallization, an isolated product with a purity of 97.5% was obtained from G. oxydans fermentation broth. The product was identified as PQQ by HPLC analysis and MS. Above all, the present research developed a simple and efficient method for the separation of PQQ from fermentation broth. [ABSTRACT FROM AUTHOR]