Fertilization is crucial for restoring and enhancing the productivity of degraded grasslands; however, the enduring impacts of a one-time fertilizer application on the vegetation and soil quality in alpine grasslands are not well understood. This study sought to assess the long-term effects of a one-time application of nitrogen and phosphorus fertilizers on the vegetation and soil physicochemical properties in alpine perennial grass-mixed grasslands that have been established for over two decades. The experiment used a randomized block design with four levels each of nitrogen (N₀: 0, N₁: 50, N₂: 100, N₃: 200 kg N/hm²) and phosphorus fertilizers (P₀: 0, P₁: 65, P₂: 117, P₃: 210 kg P₂O₅/hm²), along with their combinations, yielding a total of 16 treatment combinations. Grassland productivity and soil physicochemical properties were assessed in the first and third year after fertilization (2021 and 2023, respectively). The findings indicated that the elevated nitrogen level (N₃) notably enhanced aboveground biomass (AGB), as well as soil organic matter (SOM), available nitrogen (AN), and available phosphorus (AP) levels in 2021. The AGB was still significantly higher than the other treatments at medium and high phosphorus levels (P₂ and P₃), as well as AN, AP, and soil total phosphorus (TP) contents in 2023. There was a significant correlation between nitrogen and phosphorus fertilizers and AGB, SOM, and AN, respectively; phosphorus fertilizer showed a significant association with AP and total phosphorus (TP); nitrogen-phosphorus interactions substantially impacted SOM and total nitrogen (TN) levels, and inter-annual correlations were significantly linked to AGB, SOM, and AN, respectively. Nitrogen and phosphorus fertilizers promoted all measured indicators in 2021, while phosphorus fertilizers still significantly enhanced AGB, SOM, and TN in 2023, indicating that the legacy effect of phosphorus fertilizers was greater than that of nitrogen fertilizers. The structural equation model revealed that nitrogen fertilizer effects were most pronounced in the first year, especially at high nitrogen and medium phosphorus levels (200 kg N/hm² and 117 kg P₂O₅/hm²), whereas phosphorus fertilizer significantly influenced AGB and indirectly increased below-ground biomass via available phosphorus in 2023. The effects of phosphorus fertilizers continued into the third year, particularly with the low-nitrogen and high-phosphorus combinations (50 kg N/hm² paired with 117 and 210 kg P₂O₅/hm²), demonstrating greater endurance. Combining economic inputs, a single application of high phosphorus with low nitrogen yielded better fertilization and legacy effects. The results of the study can provide an important reference for cultivation and restoration practices in degraded mixed-grass alpine grasslands.