The concentration of two odorous compounds (geosmin and 2-methylisoborneol MIB) in intensive cultivation freshwater fish ponds of Beijing were detected by coupling HSPME with GC-MS, and the biomass of the phytoplankton and actinomycetes in the ponds were investigated at the same time. The relationship between concentration of odorous compounds and biomass of phytoplankton and actinomycetes was researched. The results show that geosmin as the main composition of odorous compounds was found in all ponds with its concentration from 1.22 to 35.58 ng•L-1, MIB was found in some ponds with its concentration from 1.39 to 6.00 ng•L-1. Algae of 6 phylum and 22 genera was determined in the ponds with its biomass from 17.33 to 178.34 mg•L-1, of which Bacillariophyta and Euglenophyta were dominant species. Four genera of actinomycetes with gross biomass from 0 to 76×104 ind•L-1 were found in the ponds, of which Streptomyces was dominant. Regression analysis between the concentration of geosmin and the total biomass of dominant algae was positive. Melosira granulata and Cyclotella striata probably were main microorganism causing off-flavour in Beijing′s intensive cultivation freshwater fish ponds in summer and autumn; Euglenophyta and other algae probably played a little role in causing off-flavour.