Soil aggregates with spatially heterogeneous microenvironments influence microbial communities and mineral protection in agricultural soils and play a pivotal role in soil organic carbon (OC) turnover. However, the mechanisms through which conservation practices affect microbial properties and mineral protection to regulate soil OC accumulation at the aggregate scale has not been determined in the black soil region of Northeast China. Here, we investigated the potential mechanisms of soil OC accumulation in two sets of conservation (Cons) and conventional (Conv) soil samples: (1) Cons (no-tillage with straw mulching) and Conv (rotary tillage with straw removal) in a Phaeozem (Lishu County) and (2) Cons (rotary tillage with straw incorporation) and Conv (rotary tillage with straw removal) in a Chernozem (Da'an County). The soil aggregates were classified into three fractions: macroaggregates (0.25–2 mm), microaggregates (0.053–0.25 mm), and silt and clay (< 0.053 mm). Cons significantly increased soil OC by increasing macroaggregate-associated OC. Cons significantly increased the concentrations of free iron oxides (Fed), iron-bound OC and calcium-bound OC in macro- and microaggregates (except in calcium-bound OC within microaggregates in Lishu) and increased exchangeable calcium (Caexe) in Da'an. Additionally, Cons significantly increased the relative abundance of Gemmatimonadota in functionally and topologically important (FTI) taxa within macroaggregates. In Da'an, the relative abundance of Ascomycota in FTI taxa within the macroaggregates and microaggregates was significantly greater in Cons. Cons significantly reduced microbial network complexity (except in microaggregates in Lishu). Structural equation modeling indicated that conservation practices regulated stable OC pools accumulation through mineral protection (mainly Caexe and Fed) and network complexity to increase macroaggregate-associated OC. Our findings emphasize the joint role of soil minerals and microbes in increasing soil OC through the modulation of macroaggregate-associated OC accumulation, which has important implications for enhancing soil quality and improving agricultural sustainability.