Soil organic carbon (SOC) has various pools with different stabilization mechanisms. It is unclear how these SOC pools respond to various mineral and organic amendments depending on a large climate-soil gradient. Here, we studied in three zonal soils: Ferralic Cambisol (subtropic), Calcaric Cambisol (warm-temperate) and Luvic Phaeozem (mid-temperate) under 23-year mineral, straw and manure amendments. Six SOC sub-pools were isolated: unprotected, physically, chemically, biochemically, physico-chemically and physico-biochemically protected pools. Compared to initial level, SOC and most sub-pools increased in the three soils under manure application (p < 0.05), but little under straw and mineral amendments. The Luvic Phaeozems had much higher sequestration efficiencies of bulk SOC (27%) and its five sub-pools (5–7%) more than the Calcaric Cambisol (9%, 1–2%) and Ferralic Cambisol (9%, 0.5–1%). In contrast, Ferralic Cambisol had highest sequestration efficiency of unprotected pool (7%). The Calcaric Cambisol had divergent patterns of the six SOC pools compared with Luvic Phaeozems and Ferralic Cambisol, due to the low clay content. With the build-up of bulk SOC, the building-up abilities of non-protected, physically-, chemically- and biochemically-protected pools depended on soil type, while the building-up abilities of physico-chemically- and physico-biochemically-protected pools were convergent (12–19%) among soils. In conclusion, the Luvic Phaeozems had much higher build-up ability of bulk SOC and most sub-pools than the other two soils. With the build-up of SOC, the physico-chemically- and physico-biochemically-protected pools (most stable) had convergent response rates among soils, while the other pools had divergent response rates.Graphical