The strategies of substituting inorganic fertilizers with organic fertilizers have been shown to significantly impact the dynamics of soil organic carbon (SOC) combating soil degradation and climate changes in intensive vegetable production. However, the underlying mechanisms and comprehensive assessment of environmental consequences are not fully understood. We conducted a five-year field experiment in the Yangtze River Delta Alluvial Plain, China, four fertilization treatments were established at equal nitrogen (N) levels: sole mineral fertilizers (SN); organic substituting 20 % (M1N4), 50 % (M1N1), and 100 % (SM) of mineral N fertilizer with organic fertilizer. Soil carbon (C) pools, physical and chemical composition of SOC, and C footprint were measured based on soil aggregates, 13C nuclear magnetic resonance spectroscopy, and life cycle assessment to investigate the effects of organic substitution on SOC quantity, quality, and environmental implications. Our results showed a significant increase in SOC content, particularly in the M1N1 treatment. This increase was attributed to changes in soil properties, an elevation in dissolved organic C content, and improved SOC stability. Specifically, organic substitution increased the proportion of macroaggregates, content of lignin phenols, and enrichment of alkyl C groups. Based on life cycle assessment incorporating field measurements, the average C footprint ranged from 1.82 to 2.58 CO2 kg eq kg−1 vegetable in the five-year experiment, primarily influenced by transportation and fertilizer manufacturing. Partial organic substitution reduced the C footprint by 6.2–10.1 %, while the SM treatment increased it by 0.54 CO2 eq kg−1 vegetable, and the M1N1 had the lowest C footprint at 1.82 CO2 eq kg−1 vegetable. As a whole, this approach of substituting 50 % of mineral N with organic fertilizers serves as a viable strategy to bolster soil C stabilization, promote C accumulation, and mitigate the C footprint linked to intensive vegetable production in subtropical regions.