Straw return directly increases carbon inputs, enhancing soil organic carbon (SOC) stocks. However, long-term straw return leads to carbon saturation in the topsoil (0–20 cm). While most studies focus on the topsoil, the effects of long-term straw return on deep soil (100–200 cm) carbon sequestration remain poorly understood. This study investigated carbon dynamics in an arid region by analyzing 0–200 cm soil profiles under different straw return treatments: control (uncultivated) and cotton straw return for 5 (SR5), 10 (SR10), and 20 years (SR20). Straw return significantly improved soil properties by reducing electrical conductivity (EC), increasing nutrient availability, and enhancing bacterial activity. SR20 resulted in the most pronounced SOC increase (18.6–252.7%) across the entire profile and significantly enhanced soil inorganic carbon (SIC) (27.7–52.7%) in deep layers. In contrast, SOC in the topsoil (0–20 cm) increased initially but plateaued after 5–10 years. Principal component and random forest analyses showed that SOC sequestration was primarily driven by sucrase, urease, available phosphorus, dissolved organic carbon (DOC), microbial diversity indices, and available calcium (p < 0.05), while SIC dynamics were significantly influenced by sucrase, urease, DOC, CO₂ emissions, available calcium, and EC (p < 0.05). These findings underscore the importance of exploring subsoil carbon sequestration mechanisms in arid ecosystems.