The soil organic carbon (SOC) and nitrogen (N) in the Yunnan Province, southwestern China, is related to the complex topography and multiple vegetation zones. However, the variation in SOC and total nitrogen (TN) stocks under different vegetation types and altitudes in the mountainous regions in Yunnan is still unknown. This study aimed to investigate the spatial distribution of SOC and TN stocks affected by different vegetation types and altitudes within three soil depths (0–20 cm, 20–40 cm, and 40–60 cm) and to determine the factors controlling the SOC and TN stocks across the mountainous regions in western Yunnan. Nine vegetation types, including tropical rainforest (TR), tropical monsoon forest (TM), broad-leaved evergreen forest (BLE), evergreen coniferous and broad-leaved mixed forest (ECB), broadleaved deciduous forest (BLD), coniferous forest (CF), alpine shrub meadow (ASM), dark coniferous forest (DC) and alpine meadow (AM), along with an altitude gradient (600–4500 m), were selected. The results showed that the SOC and TN contents decreased with increasing soil depth in most vegetation types, except DC. Soils under different vegetation types with pH ranging from 3.25 to 3.74 and 5.10 to 6.68 had significantly higher SOC stocks than soils with pH ranging from 3.99 to 5.09 (P < 0.05). The SOC and TN stocks were positively correlated with the mean annual temperature and mean annual precipitation. Higher SOC stocks (64.01–139.88 Mg ha⁻¹) and TN stocks (23.42–49.36 Mg ha⁻¹) were observed in CF, ASM, DC and AM with higher altitudes (3600–4500 m) than other vegetation types with lower altitudes (600–3600 m). The significant linear relationship between SOC and TN stocks (P < 0.01) demonstrated that most of the variations in TN are related to the changes in SOC storage, and the accumulation of SOC could influence TN stocks. Our results also suggest that vegetation type, altitude and pH could be the major factors controlling the spatial distribution of SOC and TN in mountainous regions.