Understanding the temporal changes of soil organic C (SOC) pools and microbial residues is essential for clarifying SOC dynamics in agroecosystems; however, this information remains largely unclear in greenhouse vegetable production (GVP) systems. Here, based on information of SOC pools (i.e., oxidizable organic C pools) and microbial residue C (MRC, as indicated by amino sugars differentiation), a 10-year (2009–2019) field experiment with fertilization was conducted to evaluate how fertilization alters SOC dynamics in a GVP field in Tianjin, China. The experiment includes four treatments (equal N, P₂O₅, and K₂O inputs): 100% chemical N (N₁₀₀), 50% substitution of chemical N with manure-N (N₅₀M₅₀), straw-N (N₅₀S₅₀), and manure-N plus straw-N (N₅₀M₂₅S₂₅). Results showed that the values of SOC, lability index, and C management index increased and decreased linearly with time in N₅₀M₅₀- and N₁₀₀-amended soils, respectively, which were mainly induced by the changes in labile C fractions. Based on logistic regression models, we found that these indices in straw-amended soils (N₅₀M₂₅S₂₅ and N₅₀S₅₀) were rapidly increased between 2009 and 2013, and then approach steady levels between 2015 and 2019. These findings suggested that we should guarantee enough C inputs to maintain the level and quality of SOC, otherwise it will cause C loss in the unique GVP soils. Besides, straw-amended treatments increased MRC contents and enlarged their contributions to SOC sequestration, whereas these indices in N₁₀₀ treatment decreased linearly with the time of fertilization. In conclusion, long-term chemical application alone was not beneficial for SOC accumulation, whereas organic amendments brought several benefits for SOC sequestration in GVP soils. Our results implied that C sequestration in GVP soils is to a large extent determined by the amounts and time of fertilization.