Thinning is an important silvicultural practice for improving the productivity and wood production in plantation forest. Different intensities of thinning management can affect tree growth and alter soil nutrient effectiveness, thus affecting soil fungal community structure and diversity. Our objective is to determine the soil factors and their regulatory mechanisms that influence stand growth by thinning, and to provide data to support the establishment of large diameter timber cultivation technology for Picea koraiensis. In this study, we conducted medium- and high-intensity thinning in 43a P. koraiensis plantation middle-aged forests and investigated the growth indexes, soil physicochemical properties, and fungal community diversity in rhizosphere and non-rhizosphere soils of the stands after thinning at different densities (904 plants/ha for control, 644 plants/ha for 30% thinning intensity, and 477 plants/ha for 50% thinning intensity). The results showed that all growth indicators (annual growth of tree height, diameter at breast height, height under live branches and crown width) of the plantation after high-intensity thinning (477 plants/ha) were higher than those of the control (no thinning, significant) and medium-intensity thinning (644 plants/ha). Mycorrhizal infection rate was higher at the beginning of the growing season than at the end of the growing season, and increased slightly with decreasing stand density. Compared to the control, all medium- and high-intensity thinning treatments significantly improved soil nutrient content (P < 0.05), including total carbon, total nitrogen, total phosphorus, total potassium, Available phosphorus and Available potassium. Fungal diversity was higher but lower in abundance than the control in both rhizosphere and non-rhizosphere soils after thinning. The number of OTUs and fungal richness and diversity indices of non-rhizosphere soil fungi were higher than those of rhizosphere soil fungi. In conclusion, this study provides new evidence that reasonable intercalation can increase the radial and vertical growth of P. koraiensis plantation forests and promote the diversity of subsurface soil fungal communities. It is shown that thinning intensity regulates biogeochemical cycles in P. koraiensis plantation ecosystems by affecting soil nutrients and fungal community structure. Therefore, 50% thinning intensity can be used to increase timber production in plantation forests during large diameter timber cultivation of P. koraiensis and improve predictions associated with achieving long-term forest management strategies.