Background <p>Agroforestry systems support a range of ecosystem-based management for balancing sustainable land use and biodiversity conservation. However, drivers of woody species diversity and carbon (C) storage potential in agroforestry systems and their relationships are still poorly investigated. This study aimed to (i) examine the influence of agroforestry systems on woody species diversity and C storage in various pools; (ii) identify ecological drivers of woody species diversity and its relationship with aboveground carbon stock, and (iii) explore the effect of agroforestry systems on soil organic carbon (SOC) distribution in the soil profile.</p> Methods <p>A random sampling method was employed to collect vegetation and soil data. A total of 35 plots were established in three agroforestry systems, including homegarden, live fence, and woodlot. A total of 70 composite soil samples were taken for SOC determination. The data were analyzed using ANOVA to determine differences in woody species diversity and carbon stocks among agroforestry systems. Additionally, multiple linear regression was used to test the effects of elevation and agroforestry systems on species richness and their linkages with aboveground carbon stock.</p> Results <p>The woody species diversity was significantly (<i>p</i> &lt; 0.001) different among agroforestry systems. Homegardens had higher species richness than woodlots and live fences. Shannon-Wiener's diversity was higher in live fences (2.38) and lowest in the woodlots (1.9). Elevation and agroforestry systems had a significant effect on species richness. Aboveground biomass carbon (AGC), belowground biomass carbon (BGC), SOC, and total carbon (TC) varied significantly among agroforestry systems. The TC stock (197&#xa0;Mg C ha⁻¹) of the homegardens was significantly higher than in woodlots (135&#xa0;Mg C ha⁻¹). The AGC and total biomass C (TBC) in the homegardens were estimated as 57.6&#xa0;Mg C ha⁻¹ and 15.7&#xa0;Mg C ha⁻¹, respectively, and were significantly higher than live fences. SOC concentration&#xa0;showed a decreasing pattern across soil depth under each agroforestry system, with the most pronounced decline observed under homegardens. Woody species diversity had a significant positive effect on aboveground carbon.</p> Conclusions <p>The results revealed differences among agroforestry systems in maintaining species diversity and carbon storage. Therefore, we suggest that the promotion of agroforestry should focus on differences among systems as a part of biodiversity conservation and climate change mitigation.</p>