Accordingly, it is of importance to study the action mechanisms of soil temperature on the growth of flue-cured tobacco in order to avoid disease incidences. The mulching methods with different covering and mulching materials were adopted to adjust root system temperature of flue-cured tobacco in the experiment, which consisted of six treatments, greenhouse film mulching, rice straw + greenhouse film mulching, soil-mulching plastic film mulching, rice straw mulching, rice straw mulching + sun-shading net covering and sun-shading net covering, and hence to study the physiological and ecological effects of different root system temperatures on flue-cured tobacco. The results indicated that the accumulative temperature of 400 °C in early growth of tobacco seedlings was critical for nurserying vigorous tobacco seedlings. The accumulative temperature of more than 400 °C could result in the rank growth characterized by deteriorated growth and physiological traits and low dry-matter accumulation although it was capable of increasing the plant heights and root lengths of tobacco seedlings; as the soil accumulative temperature increased with the accumulative temperature for tobacco seedlings below than 400 °C, various growth and physiological traits became favourable and vigorous growth resulted, which were in favour of acclimatizing the seedling for nurserying vigorous seedlings. The study also revealed that mulching materials had a close relation to the climate. Different mulching materials showed a strong temperature-increasing effect at a high air temperature. The combined mulching of plastic film and rice straw was a mulching method that combined organic and inorganic materials, and complemented each other in temperature-increasing effect, and thus it would be of certain value in preventing the cold damage often occurring after seedling transplanting of flue-cured tobacco.