In order to solve the obstacle of low temperature affecting the harvesting of tobacco leaves in the late growth period of flue-cured tobacco in northeast China, and to improve the quality of tobacco leaves, risk warning levels of low temperature disaster were divided into normal, low risk, medium risk and high risk. When “medium risk” and “high risk” approach (first 2 d), tobacco plant cutting and shading water-cultivated methods were taken, and the effects of economic traits, appearance quality, chemical composition content, and sensory quality of the cured tobacco leaves were analyzed. The results indicate that compared to conventional harvesting, under low temperature disaster risk warning level below medium risk, the loss rate of bad-cured tobacco was decreased by 8.5%, and the total loss rate of flue-cured tobacco was reduced by 12.6% when harvested using tobacco plant cutting and shading water-cultivated method; and the total score of appearance quality evaluation was increased by 0.06 points, but the improvement in appearance and sensory quality was not significant. Under high risk low temperature disaster warning level, with tobacco plant cutting and shading water-cultivated method, the loss rate of bad-cured tobacco was decreased by 55.1%, the total loss rate of flue-cured tobacco was decreased by 70.2%, and the proportion of high-grade and medium-grade tobacco increased significantly by 78.7% and 57.2% respectively, compared to conventional harvesting; and the total score of appearance quality evaluation was significantly improved by 0.58 points, the two sugar ratio and sugar-base ratio was significantly higher, which improved the coordination of chemical components and the sensory quality of flue-cured tobacco. It is recommended that when the low temperature disaster risk warning level is “medium risk” and below, conventional tobacco harvesting methods should be used for tobacco leaves below the mature standard in the field; when the “high risk” is approaching, the method of tobacco plant cutting and shading water-cultivated should be adopted to achieve the goal of disaster reduction and income protection.