The conversion of open fields to greenhouse cultivation leads to an increase in the amount and frequency of fertilization, as well as an increase in tillage intensity, which significantly affects soil organic carbon turnover and sequestration. In this study, four types of soils were selected in the coastal area of southeast China based on a sequence of greenhouse cultivation years of 0, 8, 18, and 36. The study fractionated the soil into four organic fractions: free mineral-associated organic carbon (f-MAOC), occluded mineral-associated organic carbon (o-MAOC), free particulate organic carbon (f-POC), occluded particulate organic carbon (o-POC), using particle size and density separation. The organic carbon content and natural abundance of ¹³C were measured for each of these fractions, as well as for the bulk soil. Key findings include a significant increase in bulk soil organic carbon with extended greenhouse cultivation, although differences between 18 and 36 years were not significant (27.4 g kg^-1 and 31.7 g kg^-1 respectively). o-MAOC and o-POC contents increased initially, then declined after 18 years. Notably, f-POC content significantly rose after 36 years, reaching 9.91 g kg^-1. The δ¹³C values for f-MAOC, o-MAOC, and f-POC showed similar increasing trends, peaking after 18 years. The carbon flow analysis revealed the main carbon turnover pathway from f-POC to o-MAOC, with reverse transfers occurring after 18 and 36 years. It highlighted a saturation limit in the sequestration capacity of occluded organic carbon and significant accumulation of labile organic carbon due to long-term greenhouse cultivation. These findings offer new insights into carbon management in agricultural soils.