Tropical peatlands serve as huge carbon (C) pools in the global C balance, and degradation due to agricultural use is a major concern. The objective of the present study was to examine the relationship between the C loss rate in agriculturally drained tropical peat soils in relation to groundwater level (GWL) and the chemical structure of the resulting soil organic matter (SOM). Soil mesocosms containing three peat soils collected from three forest types in Malaysia, Mixed peat swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests, which are classified based on dominant plant species, species diversity, and forest structure, were buried in an oil palm plantation for a period of five years. Soil samples packed in the top layer (0–20 cm depth) and the bottom (60–80 cm depth) layer were then analyzed and the results were compared with the initial values for these soils. Weight loss, total C and N contents, ash content, and pyrophosphate solubility index (PSI; an index of the degree of humification) were measured. Changes in the chemical structure of the SOC were investigated using solid-state 13C nuclear magnetic resonance (NMR) spectroscopy with phase-adjusted spinning side bands and thermally assisted hydrolysis and methylation-gas chromatography/mass spectrometry (THM-GC/MS). The C loss in the MPS forest soil, 2–12%, was smaller than that in the ABt and ABg forest soils, 20–37%, especially in the bottom layer. The higher C loss in the ABt and ABg soils, without significant difference between the top and bottom layers, can be attributed to the greater accumulation of less decomposed plant components as evidenced by the larger yields of lignin-derived phenols and polysaccharide-related compounds in THM-GC/MS analysis. The C composition as estimated by 13C NMR did not vary during incubation of the ABt and ABg soils while the yields of lignin-derived and other phenols as well as polysaccharide-related compounds in THM-GC/MS were decreased, especially in the top layer. These findings suggest that plant components with a low degree of decomposition are susceptible to drainage regardless of their structure. The progression of the oxidative degradation of lignin in the top layer of all soils was also suggested by the increases in PSI and the vanillic acid/vanillin ratio. The % O-alkyl C and % alkyl C may control the rate of C loss positively and negatively, respectively. PSI also appears to be useful for roughly estimating the decomposability of tropical peat SOM in various GWLs.