Soil carbon stability is vital for maintaining the global carbon cycle balance, biodiversity conservation, and sustainable agriculture. While the earth’s climate is experiencing unprecedented changes in recent years and will be more unpredictable in the future, it is urgent to determine the factors influencing soil organic matter content and its composition and stability, in order to ensure the soil health and food security. Agricultural management and treatments including organic treatments, tillage, crop rotation, and nutrients management are critical components that are closely linked with soil carbon retention, composition, and stability. Rodale Institute, located in Kutztown, Pennsylvania, has established a program that compares the organic and conventional cropping systems in a field trial since 1981, called Farming System Trial (FST). Total of 72 soil samples collected from FST in 1981, 2007, and 2020 will be analyzed in this study using the simultaneous thermal analysis (STA) of Thermogravimetry (TG) and Differential Scanning Calorimetry (DSC) coupled with the evolved CO2 gas analysis, to investigate and compare the long-term changes in soil organic matter and SOC thermal stability between conventional and organic agricultural systems. Statistical methods including Analysis of Variance (ANOVA) and Principal Component Analysis (PCA) were performed in R to analyze the data. Results have revealed that the soil carbon differs the most in 2020, since it is 12 years after the till and no-till separation, large variance in mean and is significantly distinct among three different treatments. Analysis of several indicators across various soil groups indicates that there is no significant difference attributable to the treatment with regard to carbon quality. Long-term observations should be conducted with consistently controlled treatment groups for tillage and systems to detect more pronounced patterns and differences.