Manure application is an effective measure to improve soil organic carbon (SOC). While the role of microbial necromass carbon (MNC) from manure on SOC and soil aggregate stability in saline-alkaline soils is less studied. In Yellow River Delta, a field experiment was implemented including: (1) CK: no fertilizer; (2) NPK: only mineral fertilizer applied as N 210 kg ha- 1, P 105 kg ha- 1 and K 135 kg ha- 1, respectively; (3) NPKC1: manure (500 kg C ha- 1) plus NPK; (4) NPKC2: manure (1000 kg C ha- 1) plus NPK; (5) NPKC3: manure (2000 kg C ha- 1) plus NPK. Manure application significantly increased the mean weight diameter (MWD) of soil aggregates in 0-40 cm soil. This was due to MNC with manure application was increased by 20.0%, 33.7%, 40.0% in 0-20 cm soil and 21.4%, 41.8%, 50.0% in 20-40 cm soil over CK treatment, which significantly increased the contribution of MNC to SOC. SOC was significantly increased by 5.3%, 11.7%, 7.5% (0-20 cm soil) and 20.6%, 28.6%, 31.7% (20-40 cm soil), which was contributed 76.7% and 89.5% variation of soil aggregates in two soil profiles. In addition, SOC was highest in NPKC2 and NPKC3 treatment, and there was no significant difference between them. Meanwhile, humus and OC functional groups had a similar trend with SOC. Appropriate manure application promoted the contribution of MNC to SOC, and was the best measurement to improve the formation of aggregates. It is crucial for soil sustainable utilization and agricultural production.