The depth distribution of soil properties are governed by several interacting factors including land use types (LUT) and agro-climate (AgC) factors. Yet, there is little information on the effects of LUT, AgC and their combination on soil properties along depth, which this study aimed to investigate. We collected a total of 36 composite soil samples using the manual percussion of a steel core tube layer by layer vertically up to 30 cm in sites representing both highland and lowlands, and analyzed for selected soil properties. A significant main effects of LUT on the depth distribution of bulk density (BD), Ca, Na, K and Cu, and AgC on soil texture, pH, EC, Ca, Na, K, P, Mn, Fe and Cu were noted. The two-way ANOVA analysis also revealed the significant effects of both LUT and AgC on the depth distribution of BD, Na, K, Cu and EC, reflecting their influences on the paths associated to bio-geo-recycling processes. Compared to crop and forestlands, the average SOC and Fe were lower while EC, CEC, Ca, Na, K, P, Mn and Zn were higher in homegarden located in highland than lowland, possibly the acid nature of the highland soil may make the extractable cations available. SOC was not significantly influenced by AgC, LUT and their interaction effect. Based on the Elemental Enrichment Ratio (EER), the SOC was concentrated in the upper surface soil in forest and cropland located both in highland (1.79, 1.33) and lowland (1.80, 1.57), respectively. The reverse propagation pattern SOC depth distribution in soils under homegarden with EER of 0.7 (highland) ad 0.8 (lowland) showed that implementing such system can accelerate carbon sinking and safely store it in subsoil. Also, diversified species composition associated with respective root architectures in the homegarden system, make it an efficient soil nutrient management, which should be widely promoted.