Soil labile organic carbon (C) fractions play a key role in agricultural soil fertility. However, the effects of long-term organic substitution regimes on soil organic carbon (SOC), its labile fractions, stability, and vegetable yields as well as the relationships among these factors in the open-field are less well-studied. Hence, the objective of this study was to analyze the effects of long-term organic substitution regimes on SOC sequestration, labile C fractions [particulate organic C (POC), microbial biomass carbon (MBC), dissolved organic C (DOC), and readily oxidizable C (ROC)], SOC stability, the C pool management index (CMI), and vegetable yields in a long-term (13 years) open-field experiment. Five treatments were examined: 100% chemical nitrogen fertilizer (CN), substituting 25% of the chemical N with manure (MN) or straw (SN), and substituting 50% of the chemical N with manure (2MN) or manure plus straw (MSN). Compared to the CN, organic substitution treatments increased the average yields of vegetable, the SOC, the labile C fractions’ contents, and the C pool management index (CMI) to varying degrees, but only MSN reached significant levels for these factors. However, the MSN treatment had a significantly lower C stability index (SI) than the CN. ¹³C-NMR analyses also confirmed that organic substitution treatments increased the proportion of O-alkyl C and the OA/A, but reduced SOC stability. Pearson correlation analysis and the partial least squares path model indicated that labile C fractions were the mainly direct contributors to yield and SOC stability. Overall, substituting 50% of the chemical N with manure plus straw is a relatively ideal fertilization practice to improve vegetable yields and enhance C activity in an open field.