The molecular diversity of soil organic matter (SOM) is considered to be a critical factor influencing soil organic carbon (SOC) persistence, and is found to show a positive relationship with SOC in many upland soils with relatively low SOC concentrations. However, the SOM diversity-SOC relationship remains under-investigated in high-SOC soils such as wetlands, which exhibit divergent SOC accumulation mechanisms compared to upland soils and may induce contrasting shifts in SOM composition during drainage-induced SOC changes. Here we utilized three contrasting wetlands (i.e., two fens and a bog) that encompassed a wide SOC range and experienced decades of artificial drainage to investigate shifts in SOM diversity after drainage. The molecular diversity of SOM was assessed based on SOM pyrolysis products using pyrolysis–gas chromatography-mass spectrometry, and its influencing factors (including plant inputs, soil minerals, and extracellular enzyme activity, etc.) were evaluated. We observed divergent responses of SOM diversity to long-term drainage in the investigated wetlands. While SOM diversity increased with SOC concentration in the low-SOC (i.e., ≤ 60 mg g^-1 soil) fen after drainage, it did not change in high-SOC (i.e., > 60 mg g^-1 soil) wetlands after drainage regardless of SOC variations. While plant inputs (e.g., root mass) drove SOC accumulation in these wetlands, microbial processing rather than plant inputs dominated increases in SOM diversity, thereby resulting in the decoupling of SOC concentration and SOM diversity in high-SOC soils. These findings suggest that SOC and SOM diversity had a non-linear relationship in divergent soils. In organic-rich soils such as peatlands, SOM diversity did not increase with SOC accumulation after drainage, in contrast to low-SOC soils. Our study provides a novel, molecular diversity-based perspective on understanding wetland SOC stability in the context of drainage caused by increasing human activity and/or climate changes.