Moderate deficit irrigation can improve lignin metabolism, thereby increasing wheat yield and lodging resistance. The moisture-sensitive variety Xinchun 22 (XC22) and drought-resistant variety Xinchun 6 (XC6) were used as experimental materials. We set mild drought (T1, J1 and 60–65% FC, where FC is the field capacity) and moderate drought (T2, J2 and 45–50% FC) during the tillering stage (T) and the jointing stage (J). We used conventional drip irrigation as a control (CK and 75–80% FC). The results show that the activity of lignin synthesis-related enzymes decreased with the growth process, while the accumulation and monomer content of lignin increased under different water treatments. The lignin metabolism and morphological characteristics of XC6 were higher than those of XC22. Under the same processing conditions, the indicators of XC22 showed more significant changes and were more sensitive to changes in the moisture content. Compared with other treatments, the stem thickness and wall thickness of the J1 treatment increased by 0.86–23.49% and 1.72–23.58%. The yield of the T1 treatment was the highest, increasing by 3.05–44.06% compared to other treatments. In addition, by improving PAL, H-type lignin monomers, S-type lignin monomers, stem thickness and lignin metabolism, grain yield can be increased. After mild drought during the jointing stage, J1 significantly improved the lignin metabolism capacity of the stem, increased stem thickness and wall thickness, and was beneficial for improving lodging resistance. The T1 treatment favored the improvement of the production capacity of assimilates, thus promoting a high yield of spring wheat.