Soil inorganic carbon (SIC), especially pedogenic carbonates (PIC), plays a role in carbon sequestration in arid and semi-arid regions, yet its coupling with soil organic carbon (SOC) fractions and microbial processes remains poorly resolved. To address this, we collected soil samples in maize- and cotton-based systems at Bole and Wuwei in Northwest China. We explicitly distinguished stable SOC (mineral-associated OC, MAOC; heavy-fraction OC, HFOC) from labile SOC (particulate OC, POC; light-fraction OC, LFOC; dissolved OC, DOC) to evaluate their separate relationships with inorganic carbon pools. We found that Bole maize soils were enriched in SIC, PIC and dissolved inorganic carbon (DIC) and dominated by stable SOC, cotton soils by POC and lithogenic carbonates (LIC), whereas Wuwei soils by labile SOC with weaker inorganic carbon association. Across sites, MAOC and HFOC were positively related to SIC, PIC and DIC, while DOC and LFOC were negatively associated with SIC. Microbial diversity and biomass were also associated with carbon fractions, with fungal diversity being particularly responsive to SOC-SIC co-variation and bacterial communities more strongly related to inorganic carbon forms and pH. Meanwhile, microbial biomass C and N correlated positively with SOC, SIC and PIC but not LIC. Furthermore, random forest and partial least-squares path modeling identified C:N ratio, cation exchange capacity (CEC), microbial status and MAOC as key predictors of PIC formation and organic-inorganic carbon associations. Collectively, these results suggest coordinated variation among organic and inorganic carbon fractions and highlight that coupling between microbial status, nutrient stoichiometry and stable SOC fractions is an important component of SIC and PIC accumulation in arid croplands of northwest China.