Long term land-use change, such as forest conversion, has been shown to strongly affect soil pore properties. The soil pores mediate soil processes and determine how soil functions. Despite their importance for understanding biological, water, and carbon stability, the properties of soil pores following long term forest conversion remain unclear in subtropical forests. We examined soil nanoscale pores in response to conversion from native forests to plantations and addressed how bacterial and fungal communities influenced soil pore properties. We found significant changes in soil pores 40 years after the conversion from native forests to Chinese fir forests or bamboo forests. The pores in mixed forest soils were similar to those in native forests, while Chinese fir forest soils contained the most pores, followed by bamboo forest soils. Chinese fir forests also had a higher surface area and volume of both total soil pores and macropores, whereas bamboo forests had a higher volume of mesopores and larger specific surface areas of the total, macro-, and mesopores. Both soil bacteria and fungi significantly influenced soil pore properties. The relative abundance of soil bacterial phyla (Planctomycetes and Verrucomicrobia), fungal phylum (Chytridiomycota), and bacterial and fungal diversity negatively affected average pore diameter. In addition, soil fungal phylum (Basidiomycota) and the total sequencing number positively affected soil mesopore volume and the specific surface areas of both total pores and mesopores. Our study demonstrated that forest conversion drove the changes in soil pores at the nanoscale. Changes in soil microbial abundance and diversity may be one of the factors that affect soil nanoscale pores, while soil fungal compositions influence soil mesopores and soil specific surface area.