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Mongolian pine is an important afforestation species widely used for ecological management in northeast China. The environment in this region is very unstable and the flora are regularly subjected to drought stress. This paper reports on the influence of inoculation with the Suillus luteus on seedlings under different water conditions. Both inoculated and non-inoculated ectomycorrhizal fungi (ECMF)-S. luteus seedlings were maintained under well-watered or water-stress conditions for 3 months. The S. luteus colonization rate under water stress was higher than that in well-watered conditions. Under water stress, inoculated seedlings had greater growth than non-inoculated seedlings. In addition, under water stress, S. luteus-inoculated seedlings had greater superoxide dismutase and peroxidase activity, higher soluble protein content, lower proline content, and lower malondialdehyde content than non-inoculated seedlings. S. luteus colonization increased the rhizosphere soil-enzyme activity and the rhizosphere soil nutrition content under both well-watered and water-stress conditions. Given the positive impact on seedling growth and physiology, S. luteus shows potential for use in the arid and semi-arid regions of northeast China for afforestation.