The optimized pre-treatment and derivatization methods were developed in this study for the determination of 1,9-decanediol by gas chromatograph in the rice root exudates. Results showed that the C18 SPE column could retain 1,9-decanediol efficiently and its relative recovery rate (82.97%) had no significant difference with that of the rotary evaporation (80.17%). This method is time-saving and fit for concentrating the identified hydrophobic BNI-compound, 1,9-decanediol, in large amount of root exudates solutions. In addition, the use of N,O-bis (trimethylsily) trifluoroacetamide (BSTFA, 200 μl) as derivatization reagent, together with 30 min heating in the oven at 60 ℃, was found to be the most efficient method for stable derivatives and high sensitivity. The linear equation was y = 34.77 x-0.90 (r = 0.999 3); the 1,9-decanediol detection limit of the method was 0.05 μg/ml; and the method exhibited good accuracy (recoveries of 94.42%) and precision (within-day precision of 2.18% and day-to-day precision of 3.01%) which could provide reference for the subsequent analysis of 1,9-decanediol in rice root exudates.