A seedling cultivation experiment was conducted in Xichang of Sichuan Province to identify the effects of fertilization times and clipping on seedling quality. The experiment used a factorial treatment design with fertilization method × clipping times (2×2) factor combination. The results showed that the seedling height, stem height, stem circumference, root volume, and dry matter mass of root, aboveground parts and the whole plant increased significantly by 28.87%, 44.08%, 26.36%, 5.22%, 27.83%, 64.32% and 57.14%, respectively, when fertilization increased from 1 time to 2 times. No significant difference between fertilization times was observed for good seedling rate, strong seedling rate, seedling recovery time and recovery rate after transplanting. Compared with those under clipping, the seedling height, stem height, stem circumference, leaf area, root volume, and dry matter mass of root, aboveground parts and the whole plant increased significantly under no clipping. The clipping increased good and strong seedling rate by 4.35 and 7.05 percentage points, respectively. No significant difference of clipping was observed for seedling recovery time and rate after transplanting. Overall, fertilization 2 times without clipping is the best, followed by fertilization 2 times with clipping. These two treatments can be recommended for tobacco production with transplanting small seedling under plastic film.