ABSTRACT This study assessed the effect of land use systems (rice-fallow, bamboo, mandarin and forest) along an altitude gradient (<500, 500–1000 and > 1000 m asl) and soil depth (0–15, 15–30 and 30–45 cm) on C stability in naturally occurring clay-organic complex (NOCOC) and their relationship with soil properties. The C stability in NOCOC (1/k) was determined from desorption rate constant (k) of humus-C by sequential extraction and was correlated with soil properties across the altitude. The C stability in NOCOC decreased (34%) with increasing soil depth from 0–15 to 30–45 cm. Across the altitudes, highest C stability in NOCOC was at > 1000 m asl (8.37 h) which was 12.7 and 9.4% higher than 500–1000 and < 500 m asl, respectively. Irrespective of soil depth and altitude, forest (5.30 h) showed the greatest C stability in NOCOC followed by mandarin (4.64 h), bamboo (4.20 h) and rice-fallow (3.85 h). Measurable soil properties could explain 90–94% variability of C stability in NOCOC across the altitude. Furthermore, C stability in NOCOC increased macroaggregate formation (0.25 mm) and ensured greater physical, chemical and microbial protection of organic C in soil.