Clearing diseased wood is a common measure used to reduce the continued spread of pine wilt disease and prevent infecting other pines. However, the impact of clearing diseased wood on the physicochemical properties of the soil is still unclear. To elucidate this matter, we conducted a series of soil experiments and observations in Changdao, mainly focused on uncut black pine, cut black pine, and the inter-forest zone. The results showed the following. (1) The soil beneath the forest underwent a transition towards the characteristics of forest and grassland after clearing diseased wood, which indicated a potential shift in the ecosystem’s structure and function. (2) Clearing diseased wood led to an increase in the soil pH of 0.15, indicating that it facilitated the recovery of acidic soil. (3) The clearing of diseased wood can coarsen the soil’s texture. Moreover, it effectively reduced the surface soil temperature (0–20 cm) in summer by 1.52 °C, as well as significantly decreasing the surface (0–20 cm) soil moisture in spring and summer by 1.3% and 2.43%, respectively. (4) Clearing diseased wood clearing can effectively modify the content of essential nutrients in the soil. It reduced the available nitrogen by 26.86 mg·kg⁻¹, increased the available phosphorus by 0.57 mg·kg⁻¹, and decreased the available potassium by 1.68 mg·kg⁻¹. Meanwhile, clearing diseased wood exacerbated soil salinization and increased the soil’s salt content by 0.70 g·kg⁻¹. The findings of this study provide scientific solutions for the sustainable ecological development of black pine forests in Changdao.