In order to find a rapid determination of organic matters and water contents in substrate of flue-cured tobacco floating system, more than 200 substrate samples were detected using Fourier transform near-infrared spectrograph, followed by the establishment of correlation models between NIR reflectance spectrum and contents of organic matters and water contents in substrate, and prediction of 12 samples. The results showed the mean deviations of organic matters and water conetents were 0.21 and -0.07, respectively. No significant difference was observed between NIR analysis and conventional methods. NIR analysis can be applied to rapid quantitive determination of substrate, which is simple, fast, low cost, of zero pollution, nonedestructive to samples, and simutaneous determination of multi-components.