Root pruning affects the ability of roots of Quercus variabilis Blume to absorb water and nutrients. Suillus grevillea can form a mutualistic symbiosis with Quercus variabilis Blume. A pot experiment in three compartments with two inoculation treatments (inoculation with Suillus grevillea and noninoculation control) and four different root pruning treatments (0, 1/4, 1/3, and 1/2 of the main root length pruned) was conducted. The shoot dry weight, root dry weight, shoot and root N, P and K contents, root morphological and physiological parameters of Quercus variabilis Blume seedlings, and soil properties were measured. The results showed that root pruning affected root endogenous hormone levels, root morphology, shoot and root nutrient absorption, and biomass accumulation. Compared with those without inoculation, the shoot dry weight, root dry weights, shoot and root N, and P and K contents of inoculated plants were greater, regardless of the degree of root pruning. The root length, root projection area, root surface area, root average diameter, root density, root volume, and root tip number increased in response to Suillus grevillea. The root auxin (IAA), cytokinin (CTK), gibberellin (GA), zeatin riboside (ZR), and salicylic acid (SA) contents were greater in inoculated Quercus variabilis Blume seedlings than in noninoculated plants. Inoculation with Suillus grevillea improved the soil microenvironment around the seedlings. Suillus grevillea can compensate for the adverse effects of root pruning on nutrient absorption, root morphological and physiological growth and the soil properties of Quercus variabilis Blume seedlings.