Application of organic material is a win-win strategy that effectively boosts soil carbon (C) storage and promotes organic waste recycling in urban ecosystems. However, the divergent responses of C sequestration to organic materials and the underlying mechanisms remain unclear. Using molecular and litterbag methods, this study examined soil organic C (SOC) content, C sequestration efficiency of organic material (CSE-organic material), microbial necromass and community composition in urban greenspaces amended with different types of organic materials. The field experiment had seven treatments: addition of green waste (GreenWaste), green waste compost (GreenWasteCompost), biogas residue (BiogasResidue), biogas residue compost (BiogasResidueCompost), peat (PEAT), biochar (BioChar), and no organic material (Control). Organic materials after 16 months application increased SOC content by 34.1–87.0% compared with the Control and presented CSE-organic material in the order: BioChar > GreenWasteCompost > PEAT > BiogasResidueCompost > GreenWaste > BiogasResidue. Aromaticity index was positively correlated with CSE-organic material, indicating that aromatic C addition had a strong capacity to enhance C sequestration. Microbial necromass increased from 2.7 g C kg−1 in the Control to 3.9–5.0 g C kg−1 under organic materials addition. Bacterial necromass was enriched in the BiogasResidue and BiogasResidueCompost treatments, primarily because of sufficient substrate that facilitated the proliferation and activity of copiotrophic Firmicutes, whereas fungal necromass was 8.8–19.1% higher in the GreenWaste, GreenWasteCompost, and PEAT treatments than that in the BiogasResidue and BiogasResidueCompost treatments, accompanying by an increasing abundance of Ascomycota. However, the contribution of microbial necromass to the increased SOC was negatively correlated with CSE-organic material, suggesting that the input of recalcitrant C weakened the role of microbial necromass in C retention. Overall, this study reveals that the efficiency of organic materials application in promoting soil C accumulation depends largely on recalcitrant C rather than microbial necromass, which highlights the important role of organic waste acting as a C source in achieving urban sustainable development.