Climate change and shrub encroachment affect nematode biodiversity, although shrub species had different effects on below-ground community. Yet, the consequences of shrub species on the nematode beta diversity under future climate change scenarios remain insufficiently explored. Here, we studied the dominant shrub effects on the beta diversity of soil nematode communities along climate gradients on the Qinghai-Tibet Plateau. We investigated soil nematode communities in 31 sites of alpine meadow ecosystems across a 1200 km × 1200 km area with widespread shrub on the Qinghai-Tibet Plateau. We found that shrubs decreased the nematode beta diversity through decreasing the nestedness component at local and landscape scales. Leguminous shrubs had stronger effects on the nematode beta diversity than non-leguminous shrub types at landscape scale. MAP and MAT both significantly increased the negative shrub effects on the nematode beta diversity, but they remained constant for leguminous shrub. The pSEM analysis showed that shrubs had direct and indirect effects on nematode beta diversity via plant species turnover. Our results showed that shrub encroachment, particularly leguminous shrubs, leads to the homogenization of nematode communities. The “warming-wetting” trend will exacerbate shrub effects on the homogenization of nematode communities on the Qinghai-Tibet Plateau. Our study provides insight into the ecological processes that maintain soil biodiversity and biogeographic patterns of soil communities on the Qinghai-Tibet Plateau.