Grassland degradation stems from disordered energy flow and material cycling caused by heavy grazing pressure. Fertilization is an effective measure to restore degraded grasslands. However, the mechanisms through which organic fertilizers influence soil nematode communities remain poorly understood. The objective of this study was to explore the correlation between soil nematode community structure and key environmental variables, and to identify the optimal local fertilization rates. This study was conducted in subalpine meadows located in the southeastern Qinghai-Tibetan Plateau, where organic fertilizer was applied for two consecutive years. The type of organic fertilizer is fully decomposed sheep manure. A total of seven treatments were established, including a no-fertilizer control group (CK) and six organic-fertilizer-application gradient groups (O1 to O6). The application rates of organic fertilizer for the gradient groups were as follows: 2250 kg·ha⁻¹, 3750 kg·ha⁻¹, 5250 kg·ha⁻¹, 6650 kg·ha⁻¹, 8250 kg·ha⁻¹, and 9750 kg·ha⁻¹, respectively. The results demonstrated that organic fertilizer significantly improved soil fertility and increased the relative abundance of phytophagous nematodes. In the soil nematode community, Aporcelaimellus, Criconemoides and Acrobeles were the dominant genera. Key environmental factors, including alkaline nitrogen (AN), soil bulk density (BD), soil pH (pH), and aboveground biomass (AGB), were identified as the primary drivers of changes in nematode community structure across different trophic types. The results of the principal component analysis (PCA) showed that O4 (6750 kg·ha⁻¹, corresponding to 135 kg·ha⁻¹ nitrogen and 67.5 kg·ha⁻¹ phosphorus) was the ideal fertilizer rate for the region. This approach aimed to provide a scientific foundation for the enhanced restoration of degraded subalpine meadows.