The optimized cultivation process of wolfberry (Lycium barbarum L.) to maintain a consistently high and stable yield relies on the prolonged use of significant amounts of nitrogen fertilizers. However, this practice leads to increased production costs and various issues, such as soil pollution and compaction. To address these concerns, a three-year field trial was conducted involving different nitrogen application rates: N1 (20% nitrogen (N) reduction, 540 kg·hm−2), N2 (medium N, 675 kg·hm−2), and N3 (20% nitrogen increase, 810 kg·hm−2). The results showed that the inter-annual growth and development of wolfberry roots had two rapid growth peaks. In comparison with the N3 treatment, the root morphological characteristics index increased significantly under the N1 and N2 treatments. Among the different diameter classes, the most significant increase in fine root length, with an average diameter between 0.4 and 0.8 mm, occurred under the N1, N2, and N3 treatments, accounting for 50.6%, 50.92%, and 47.72% of the total annual growth of root length increments, respectively. Concerning the distribution of fine roots, the active layer depth extended under the N2 treatment suggesting that medium nitrogen application favored the longitudinal extension of fine roots. Leaf nitrogen content and the chlorophyll meter values (SPAD values) in the upper part of the plant, at the tip of shoots/branches, were the most sensitive indicators to changes in nitrogen application rates. These values increased significantly with higher nitrogen application amounts. Similarly, the contents of total sugar, betaine, and β-carotene increased with increasing nitrogen application rates, while the contents of Lycium barbarum polysaccharides (LBPs) and total flavonoids decreased. Finally, based on a comprehensive principal component evaluation, the rankings for root growth and plant development under various nitrogen application treatments were as follows: N2 (1.891) > N1 (0.002) > N3 (−1.894). The results showed that both the aboveground and belowground growth and development of wolfberry plants were most optimized under the N2 treatment. These findings provide a foundational reference for constructing good root morphology of wolfberry through cultivation practices such as nitrogen fertilizer management.