This study addresses the scientific question of the spatial differentiation mechanisms of calcium carbonate (CaCO₃) in surface sediments across the 90°E Ridge in the northeastern Indian Ocean,  employing a multi-scale analytical approach to elucidate controlling factors and biogeochemical processes. Through bulk and size-fractionated (>150 μm, 63~150 μm, 38~63 μm, 25~38 μm, <25 μm) CaCO₃ contribution analyses of surface sediments from 10 stations, combined with quantitative statistical analysis of scanning electron microscopy (SEM) microfeatures, the following findings were obtained: (1) The CaCO₃ content exhibits significant spatial variability (36.95%~74.76%, mean 56.05%), forming a tripartite gradient pattern of 30%~45%, 45%~60%, and 60%~75%. (2) In regions water depths above 3000 m, the dominant CaCO₃ components are >150 μm planktonic foraminiferal shells (contribution >65%), while stations near or above the lysocline are dominated by <25 μm fine-grained fractions (contribution >58%). (3) Quantitative microfeature analysis reveals, for the first time, a co-deposition pattern of calcareous dinoflagellate fossils (relative abundance up to 73.68%) with coccoliths and foraminiferal fragments in the 25~38 μm fraction. Further investigations demonstrate that CaCO₃ distribution is governed by a ternary regulatory mechanism involving water depth-dependent dissolution effects, terrigenous clastic input, and siliceous biological dilution. This study innovatively establishes an integrated methodology of "grain-size separation-microscopic statistics-environmental interpretation," which not only refines theoretical models of CaCO₃ distribution in seamount geomorphic units but also expands the understanding of deep-sea inorganic carbon reservoirs by identifying calcareous dinoflagellate fossils as a novel carbon source. The findings provide a critical case study for comparative research on CaCO₃ preservation mechanisms in global ridge systems and offer vital scientific insights for parameterizing marine carbon cycle models through improved algorithms for size-specific CaCO₃ flux calculations.