To determine the optimal application rate of straw–organic manure that simultaneously improves soil aggregate stability and resource use efficiency, an incubation experiment was conducted to investigate the response patterns and mechanisms of aggregate stability in saline soil to combined straw–organic manure inputs. Coastal saline soil from northern Jiangsu Province was used as the test soil. Straw and well-decomposed cattle manure–based organic fertilizer mixed at a 1:1 ratio were applied as exogenous carbon sources. A no-input treatment was used as the control (CK), and five application rates (8000, 11 000, 14 000, 17 000, and 20 000 kg/hm2) were established. A 127-day laboratory incubation experiment was performed, during which soil aggregate stability, organic carbon fractions, and aggregate size–specific organic carbon contents were dynamically monitored. The results showed that:① Exogenous carbon application significantly enhanced soil aggregate stability. When the application rate did not exceed 14 000 kg/hm2, mean weight diameter (MWD) continuously increased. After the application rate reached 14 000 kg/hm2, the MWD and the carbon contribution rate of macroaggregates (>2 mm) among treatments tended to converge with incubation time. Thus, 14 000 kg/hm2 was identified as the threshold application rate of straw–organic manure–derived exogenous carbon.② Aggregate turnover exhibited periodic fluctuations consistent with the Six conceptual aggregate hierarchy model, and MWD was extremely significantly positively correlated with the proportion of large aggregates (>0.25 mm).③ Particulate organic carbon (POC) was extremely significantly positively correlated with MWD and was identified as the core fraction driving the threshold response. The final POC contents in treatments with application rates ≥14 000 kg/hm2 were significantly higher than that in CK and tended to converge.④ Combined application of straw and organic manure promoted aggregate formation by enhancing POC accumulation. An application rate of 14 000 kg/hm2 was identified as the optimal rate, achieving synergistic improvement in aggregate stability and efficient resource utilization. This study provides important theoretical and methodological support for structural improvement of saline soils.