This study investigated the relationships between the soil organic matter content (SOM), SOM thermal pools, soil properties, and tillage practices, on cropland soils of the central plateau of Switzerland. Soil samples were collected in 45 no-till and conventional tillage fields in five layers from 0 to 40 cm depth. Soil organic carbon content (SOC) and hydrocarbon compound (HC) pools were analysed with Rock-Eval® thermal analysis. In addition, the clay content was determined by sedimentation. The SOM contents were highest in 0–5 cm of no-till soils and the plough pan of tilled soils. SOM was less oxygenated and showed lower degradation under conventional tillage then no-tillage. The proportion of the thermo-stable pool was mainly explained by the SOC:clay ratio, regardless of tillage practices. Below a SOC:clay ratio of 0.08, all pools were decreasing nearly equally with decreasing SOC. Above this ratio, thermo-stable pools increased only slightly, while thermo-labile pools increased linearly with SOC:clay on the full SOC:clay range. The 0.08 SOC:clay threshold in the thermo-stable pools content corresponded to the lower threshold of structure stability determined for Swiss and UK soils, below which, on average, severely degraded structures are observed in the field. These findings suggest that a large proportion of thermo-labile pool is necessary for acceptable to high soil structure quality, to protect the thermo-stable forms from degradation, and to reach the carbon sequestration potential of the soil.