Having nursery rapeseed (Brassica napus L.) seedlings at a high density in a tray is an indispensable step to realizing mechanized transplanting for rapeseed. The reduction in seedling quality caused by high sowing density is one of the key factors affecting transplanting quality and yield. Uniconazole has been considered as a potential plant growth regulator to improve plant growth under diverse unfavorable circumstances. In two sowing densities (400 and 800 seeds per tray), an experiment was carried out between 2021 and 2022 to investigate the effects of uniconazole seed-coating treatments on pre-transplant and post-transplant seedling characteristics. The results demonstrate that uniconazole treatment can effectively reduce the high-density-induced reduction in seedling dry matter and leaf area, stem thinness, and stem and petiole overgrowth. Further evidence that uniconazole can improve seedling quality, enhance yield, and lessen yield loss due to high-density sowing was provided by yield at maturity. However, because of the uncontrolled growth during the late stage in the tray, the relative growth rate of seedlings after transplant in the transplant shock stage revealed that lower doses of uniconazole treatment have a negative effect on the seedling recovery. The results of principal coordinate analysis and partial correlation analysis proved that the yield and net assimilation rate were related to the improvement of seedling high-density tolerance by uniconazole treatment. Consequently, 500–750 mg L−1 uniconazole coating per 100 g of seeds in 5 mL is recommended by this study, considering the potential risk of seedling emergence and growth caused by an overdose of uniconazole treatment.