Woody encroachment has become a common phenomenon in arid and semi-arid grassland worldwide. Soil nematodes are important in promoting organic matter decomposition and nutrient cycling. Although the effects of shrubs on species diversity and functional indices of soil nematode communities have been well studied, the effects of shrubs on the functional diversity, phylogenetic diversity, and metabolic footprint of soil nematode communities are still not well understood. Environmental factors affecting nematode community composition at functional group level and interspecific differences in the effects of shrubs on nematode community composition remain unclear. In this study, we investigated the diversity, composition and metabolic footprint of soil nematode communities, as well as the associated soil physicochemical properties and plant community characteristics outside and inside canopies of three Caragana shrub species (Caragana tibetica, C. roborovskyi and C. stenophylla) in the Inner Mongolia. We aimed to examine the effects of shrubs on soil nematode communities, analyze whether such effects are species specific, and explore how shrubs affect the nematode community composition through environmental factors at nematode functional group level. Our results showed that Caragana shrubs had no significant effects on nematode abundance, richness and diversity, but significantly altered nematode community composition. The possible reasons were that Caragana shrubs had selective effect on nematode species, the effects of shrubs on nematode communities were likely mainly through root exudates, litter quality and other factors, not through soil physicochemical properties and understory plants. The changes in nematode composition led to significant changes in nematode community metabolic footprint. The functional metabolic footprint of nematode community under shrub canopies was higher than that in the open areas (except for C. stenophylla), indicating that soil nematode communities under shrub canopies had higher carbon use efficiency. Among the three Caragana species, C. stenophylla had highest structural footprint, suggesting that it had the strongest facilitation effects on the metabolic footprint of omnivores-predators. The changes in nematode community composition led to the significant changes in soil food web structure through nematode metabolic footprint. The soil nutrient status of C. stenophylla was better with lower disturbance level, and the soil food web was more mature and stable; the soil nutrient status of C. tibetica and C. roborovskyi was moderate with higher disturbance level, and the soil food web tended to degrade. In conclusion, Caragana shrubs altered soil nematode community composition and structure, and such changes were shrub species dependent. Changes in nematode composition caused shifts in metabolic footprints, which further led to variation in soil food web structures.