This study aimed to investigate drought resistance of the LY1306 tobacco strain. Seedlings of tobacco strains LY1306, ZhongYan 100 (ZY100) and Hong Hua Da Jin Yuan (HHDJY) were treated with polyethylene glycol (PEG)-6000 to induce osmotic stress. As validation, water-deficit-induced drought treatments, including mild drought (MD; watering 1.5 L/week) and severe drought (SD, without watering) were carried out. Changes in cell morphology, leaf water potential, antioxidant enzyme activity, as well as contents of malondialdehyde (MDA) and proline were determined for each treatment. Transcriptome sequencing was performed for the seedlings treated with 15% PEG-6000. No obvious changes were observed in morphology of LY1306 and ZY100 under osmotic or drought stress; whereas, visible wilting was observed in HHDJY. Superoxide dismutase and peroxidase activities of LY1036 and ZY100 under osmotic stress were significantly higher than those of HHDJY. Under SD, the MDA content of LY1306 was significantly lower and the proline content of LY1306 was significantly higher than that of HHDJY. Differential genes between LY1306, ZY100 and HHDJY were enriched in functions about alpha-linolenic acid, and arginine and proline metabolisms. LY1306 could increase its antioxidant enzyme activities and proline accumulation in response to drought stress, probably by regulating drought resistance-related pathways and genes.