Soil biota are critical for services and the functionality of terrestrial ecosystems. Studying the composition of total belowground soil biota across different ecological scales has become popular in recent years. Soil biota follow divergent responses to soil physiochemical properties (SPP) in different forest ecosystems; however, little is known about their comparative responses to various stand ages across different soil depths in Chinese fir (CF) and secondary natural forests (NF). The community assemblages of soil bacteria, fungi, archaea, protists, and animals were compared across three soil depths (0–10, 10–20, 20–40 cm) using five age (5, 8, 21, 27, and 40 years) chronosequences of CF and NF in Southern China. Our results revealed that with increased soil depth and stand age, a comparatively high abundance and increased diversity of soil biota were observed in the NF as compared to CF. Across different stand ages, NF had significantly higher total nitrogen, total carbon, available potassium, and a significantly high abundance of top soil biota classes i.e., Acidobacteriia, Planctomycetacia, Gammaproteobacteria (Bacteria), Agaricomycetes (Fungi), Group 1.1c (Archaea), Colpodea (Protists), and Enoplea (Animals). Similarly, a significantly high alpha diversity was recorded in NF for bacterial, protists, and animal communities. We observed that the composition of soil bacteria and fungi were more influenced by changes in soil depth and stand ages, while negligible or least changes were observed for soil animals in both CF and NF chronosequences. Correlations between soil biota and environmental factors indicated that total nitrogen and available potassium had the greatest influence on NF. Our results highlight the importance of NF for the enrichment of soil fertility and improvement in the assemblage of soil biota. These findings are important for an insightful understanding regarding the dynamics of total belowground soil biota in CF and NF that can be helpful for more sustainable forest management in subtropical ecosystems.