The Intermontane valleys interspersed with rugged landscapes represent a unique ecosystem and are the barn of the eastern Himalayas (EH). Soil organic carbon (SOC) plays an important role in controlling cropland productivity in these valleys. Despite this, very little is known about SOC inventories (content and stocks) and their complex interplay with some of the major control factors such as climate, elevation, land use, parent materials, and soil properties. Therefore, the objective of this study was to assess the relative influence of heterogeneous control factors (PL: Parent materials and land use) on the vertical distribution of SOC inventories at a homogeneous climate and altitude. For the study, I choose one of the largest but largely unexplored intermontane valleys (Barak) of the eastern Himalayas. By exposing a total of 72 profiles to the C horizon or water table, a thorough analysis of the influence of PL on SOC inventories (Dichromate oxidizable) and key soil parameters controlling vertical distribution of SOC in valley soils were determined The measured SOC content in the surface soil (0.15–0.24 m deep) varied from 0.91% to 1.42%, while in the soil profile (up to a depth from 1.19 to 1.56 m), the SOC content (PWA: profile weighted average) ranged from 0.60% to 0.97%. The surface layer represented only 15% soil profile depth, while contributing 33% of the SOC content (Dichromate oxidizable). The variation in SOC content (PWA) was higher among soil parent materials (e.g. Alluvium, pebble bedded-sandstone, sandstone intercalated with shale, and pure shale, CV> 16.0%) than in land use systems (e.g. Paddy agriculture, forest, and plantation, CV <3.0%). The SOC stock on the soil profile (PWA) ranged from 19.4 to 36.0 Mg ha−1. The total (soil profile) SOC stock varied from 67.5 to 161.1 Mg ha−1. In general, the SOC inventories increased relative to the clay content (correlation, r = 0.38–0.75, p < 0.05) and parent materials controlled the variation in surface and subsurface soils while the effect of land use was mostly limited to surface soils only. Deep soils (>1.55 m) developed on shale with higher clay content had higher SOC inventories (p < 0.05) than coarse-textured sandstone soils. Parent materials contributed to greater heterogeneity (R2adj = 77.1%) in SOC inventories compared to land use systems (R2adj = 61.7%). Therefore, in addition to land use, parent materials should be considered an important control factor in the estimation of SOC inventories and future research on C- sequestration in the intermontane valleys.