Organic matter is the core of soil fertility and plays a dual role in both acidity mitigation and fertility improvement. Acidity and poor fertility are two fundamental characteristics of cultivated land in the red-yellow soil regions of south China. Focusing on the synergistic interaction between acid reduction and fertility improvement, this paper reviewed the impact of acidity on organic matter accumulation, the techniques of combining organic and inorganic fertilizers in both dryland and paddy fields, and the aggregates-organic matter-microbes coupling mechanism with the particular attention given to the roles of aluminum and iron. Future research should emphasize the characteristics of low pH and iron-aluminum enrichment in red-yellow soils, develop new measures for synergistic acid reduction and fertility improvement, isolate synthetic microbial communities and optimize their colonization conditions, and elucidate the aggregates-organic matter-microbes coupling mechanism using multidisciplinary knowledge and new techniques.