Lodging stress results in grain yield and quality reduction in wheat. Uniconazole, a potential plant growth regulator significantly enhances lignin biosynthesis and thus provides mechanical strength to plants in order to cope with lodging stress. A field study was conducted during the 2015–2016 and 2016–2017 growing seasons, to investigate the effects of uniconazole sole application or with micronutrient on the lignin biosynthesis, lodging resistance, and production of winter wheat. In the first experiment, uniconazole at concentrations of 0 (CK), 15 (US1), 30 (US2), and 45 (US3) mg L–1 was applied as sole seed soaking, while in the second experiment with manganese (Mn) at concentration of 0.06 g L–1 Mn, 0.06 g L–1 Mn+ 15 mg L–1 uniconazole (UMS1), 0.06 g L–1 Mn+30 mg L–1 uniconazole (UMS2), and 0.06 g L–1 Mn+45 mg L–1 uniconazole (UMS3), respectively. Uniconazole sole application or with micronutrient significantly increased the lignin content by improving the lignin-related enzyme activities of phenylalanine ammonia-lyase, cinnamyl alcohol dehydrogenase, tyrosine ammonialyase, and peroxidase, ameliorating basal intode characteristics, and breaking strength. The spike length, spike diameter, spikes/plant, weight/spike, yield/spike, and grain yield increased and then decreased with uniconazole application at a higher concentration, where their maximum values were recorded with UMS2 and US2 treatments. The lignin accumulation was positively correlated with lignin-related enzyme activities and breaking strength while, negatively correlated with lodging rate. Uniconazole significantly improved the lignin biosynthesis, lodging resistance, and grain yield of winter wheat and the treatments which showed the greatest effects were uniconazole seed soaking with micronutrient at a concentration of 30 mg L–1 and 0.06 g L–1, and uniconazole sole seed soaking at a concentration of 30 mg L–1.