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Accurate assessments of soil organic carbon (SOC) and total nitrogen (TN) stocks and controlling factors are essential for understanding carbon and nitrogen sequestration in soil. In this study, we analyzed the spatial distribution and influencing factors of SOC and TN stocks to the depth of 3 m in a desert oasis ecotone of northwestern China. The study area has experienced large-scale transition of dunelands to irrigated croplands in the past 40–50 years. The results showed that the vertical distributions of SOC and TN stocks were well demonstrated by quadratic function forms. The SOC and TN stocks at 0–3 m depths in nabkha dunes were generally significantly higher than that in bare sand dunes. Additionally, after converting nabkha dunes to croplands, both SOC and TN stocks at the top 0.4 m depths increased with the extension of cultivation years, the mean SOC and TN stocks significantly increased from 0.396 to 0.992 kg·m−2 and from 0.053 to 0.096 kg·m−2, respectively. The strongest heterogeneity of SOC and TN generally appeared at top 0–0.4 m depths and decreased with the depth. The SOC and TN stocks in the nabkha dunes near the water areas were relatively higher, which may be suitable for croplands reclamation. It is noteworthy that land use brought a major influence of SOC and TN at top 0–0.4 m depths, whereas soil texture (clay and silt contents) was the main factor that controlled SOC and TN at deep soil depths (1–3 m). The results indicate that the nabkha dunes also increased carbon and nitrogen stocks throughout the entire 3 m soil profiles. While the demand for food is almost certain to increase in arid and semiarid China and other regions worldwide, the conversion from non-traditional croplands such as dunelands to croplands is likely going to continue.