A long-term stationary experiment was conducted to investigate effects of three rice-based cropping systems on total organic matter content, status of organo-mineral complexes, form and composition of humus, optical properties and acidity of HA in paddy soil derived from red earth. Results showed that the system of rice-rice-flooded fallow was higher than the paddy-upland alternation system in contents of total organic matter, heavy fraction organic matter, and HA and HA/FA ratio, but it was reverse in loosely combined humus content, ratio of loosely to tightly combined humus, E4 value and total acidity of HA contrary. In conclusion, the former contributed to accumulation of total organic matter and HA, but not to growth of HA molecules and quality of humus, while the latter did to activity of soil organic matter, complexity of molecular structure of HA, oxidation degree and aromaticity of HA, suggesting that harmonization between the humification and mineralization of soil organic matter through regular alternation of paddy and upland cropping can improve quality of soil organic matter.