The retention and availability of soil carbon (C) and nitrogen (N) significantly affect the stability and sustainability of the restored ecosystem. Research about how fine root regulates soil C and N processes is significant importance for thoroughly understanding the role of vegetation restoration and its specific application. An experiment was carried out at the vegetation restoration plot which has lasted for ten years in Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences. We analyzed the changes and relationships in plant (fine root biomass, δ¹³C, δ¹⁵N) and soil (soil organic C, total N, δ¹³C, δ¹⁵N, soil aggregates, sand content, exchangeable Ca²⁺, dissolved organic C and N, NH₄⁺, inorganic N, microbial C and N) physiochemical properties among eight vegetation restoration models, in order to clarify the effects of fine root on soil C and N retention and availability. The results showed a significant relationship between fine root and soil organic C and total N, indicating that fine root played an important role in regulating soil C and N retention. The significant relationships between fine root and soil aggregates, sand content, exchangeable Ca²⁺ and soil water content, combined with the proportion of C input derived from new vegetation, the changes and relationships of plant and soil δ¹³C and δ¹⁵N further indicated that the effects of fine root on soil C and N retention may mainly depend on improving soil aggregate structure, which enhanced the conservation and retention of the original soil C and N; while the effect of fine root organic matter inputs was weak. The results showed a significant relationship between fine root and dissolved organic C and N, NH₄⁺ and inorganic N, indicating that fine root affected soil C and N availability. The significant relationships between fine root and soil microbial C and N further indicated that fine root may regulate soil C and N availability by affecting microbes. Our results showed that the higher soil C and N concentrations in spontaneous regeneration and aboveground vegetation removal models compared with other six models. The better sequestrated soil C and N in spontaneous regeneration and aboveground vegetation removal models may be due to higher fine root biomass and nitrogen fixing plants. Together, fine root played the positive effect on the retention and availability of soil C and N during vegetation restoration in a karst slope ecosystem. Thus, well-developed roots and nitrogen fixing plants can be jointly planted during rocky desertification ecological restoration.