In order to investigate the physiological response of flue-cured tobacco to different watering conditions, the effects of water stress and water compensation on physiological characters and spectral features of flue-cured tobacco were studied with a pot culture experiment. The results showed that: 1) Under drought stress, chlorophyll and soluble protein in leaves degraded, and the photosynthetic rate and transpiration rate decreased, which resulted in the reduction of dry matter accumulation. The photosynthetic rate and transpiration rate could recover somewhat by rewatering as compensation. 2) Waterlogging also affected the physiological functions of tobacco leaf greatly, which aggravated the membrane lipid peroxidation and was more harmful than drought stress. 3) Both drought and waterlogging increased the reflectivity of visible light from tobacco plants in the region of 460-670 nm while decreased that of near infrared in the region of 780-1050 nm. Therefore, spectral characters can be used as an important means for diagnosing the extent of water stress on flue-cured tobacco.