Numerous studies have shown that appropriate nitrogen (N) positively affects wheat yield increase, while excessive N decreases stem resistance to lodging and reduce yield. In comparison, photosynthetic carbon allocation in wheat leaves plays a crucial role in yield formation (spike) and resistance to lodging (stem). This study aimed to determine why high N fertilizer increases the risk of wheat stem lodging and how N fertilization regulates photosynthetic carbon allocation to harmonize the balance between wheat yield and stem quality. We used four N levels of 0 (N0), 120 (N1), 240 (N2), and 360 kg ha−1 (N3) with Jimai 22 (JM22), Shannong16 (SN16), and Taikemai 33 (TK33) as experimental materials. Per increase of 120 kg ha−1 of N fertilizer, the breaking moment of stem decreased by 13.51–24.67%; stem nonstructural carbohydrate (soluble sugar and starch) content decreased by 1.83–5.11% and 3.59–10.23%; structural carbohydrate (cellulose and lignin) content decreased by 8.13–14.59% and 11.23–18.01%. Photosynthesis of leaves led to an increase in starch content of 30.79 mg g−1 12 h−1 during the day, and starch was continuously broken down, leading to an increase in soluble sugar content of 18.15 mg g−1 12 h−1. The stems used the soluble sugars obtained from the leaves to synthesize structural carbohydrates to ensure their quality. N application increased the content of soluble sugars in the leaves. It showed that the leaves could produce enough substrate for the stems. However, stems could not fully utilize the carbohydrates produced by leaves to synthesize sufficient lignin and cellulose, resulting in poor stem quality. Therefore, in the future, improving the ability of stems to assimilate and utilize carbohydrates will be the key to ensuring the quality of stems and improving the resistance of wheat to lodging.