2-methylisoboneol (2-MIB) and geosmin are two typical earthy-musty odour compounds in freshwater. In order to investigate the olfactory thresholds of 2-MIB and geosmin in black carp (Mylopharyngodon piceus) and bighead carp (Hypophthalmichthys nobilis), an improved and optimized pre-treatment method of adsorbing the earthy-musty odours combined with the technology of gas chromatography following microwave distillation-headspace solid-phase microextraction was developed. The fish back muscle samples were placed in vials with the 2-MIB/geosmin solution and reached the adsorption equilibrium. Some samples were evaluated by a panel of ten members using Flavour Profile Analysis (FPA) method, the remaining sample was used for instrumental analysis. In fish muscle blocks, it took 90 and 105 min to establish the absorption equilibrium of 2-MIB and geosmin, respectively. The olfactory thresholds of 2-MIB in the bodies of black carps and bighead carps were 0.35 μg/kg and 0.30 μg/kg, respectively, while the geosmin thresholds were 0.59 μg/kg and 0.51 μg/kg, respectively. The concentrations of 2-MIB and geosmin in the bodies of black carps were slightly higher than in bighead carps, which were probably caused by the differences in the body fat content and the volatility of 2-MIB and geosmin.