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The eastern Tibetan Plateau has experienced an enormous increase in afforestation over the past few decades to restore the biological environment, but the subsequent effects of different tree species on soil nutrients after afforestation were still unclear. Four typical coniferous plantations (Larix principis, Picea asperata, Pinus tabuliformis, and Picea wilsonii) were selected to investigate the differences in soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) contents and stocks, and their driving factors included environmental and soil variables on the eastern Tibetan Plateau in this study. We found that the soils under Larix principishad the highest average SOC, TN, and TP contents and stocks, whereas the soils under Pinus tabuliformiswere the lowest. The Larix principismight be the most promising planting tree species for carbon sequestration and nitrogen fixation in the future. Additionally, it was demonstrated that afforestation age was the dominant factor of SOC and TN stocks. The SOC, TN, and TP stocks of the surface soil were responsive to tree species and afforestation age, while those in deep soil were mainly influenced by environmental and soil variables. These findings indicated that planting Larix principiscould more effectively improve the potential of SOC and TN stocks. These had significant implications for carbon sequestration and future afforestation strategies on the eastern Tibetan Plateau.