Soil microbial residues contribute to a significant proportion of soil organic carbon (SOC). However, the accumulation patterns and controlling factors of microbial residues in croplands across a large scale have yet to be elucidated fully. Therefore, amino sugars, as the biomarker of microbial residues, were measured in soils collected from thirteen sites across eastern China. Variation partitioning analysis (VPA), random forest model (RF) and structural equation model (SEM) were employed to determine the contribution of mineralogical, edaphic and climatic factors to the accumulation of amino sugars in soil. Fungal-derived glucosamine increased from cooler and drier sites to warmer and wetter sites, whereas bacterial-derived muramic acid had no obvious pattern across the studied region. We present the first evidence that iron and aluminum oxides primarily explain the variation in fungal-derived glucosamine, while pH and C/N ratio play a central role in the accumulation of bacterial-derived muramic acid in cropland soils along the continental scale. The divergent controls of accumulation of fungal and bacterial necromass in cropland soils have advanced our knowledge on the assessment and prediction of microbial contributions to SOC. Results also have significant implications for enhancing the potential of organic C storage in cultivated soils.