Excessive applications of chemical fertilizers (e.g., nitrogen fertilizers) result in soil degradation, while organic manure application can alleviate soil degradation and rebuild a healthy soil. However, the effect of organic manure application on alleviating soil degradation over long-term fertilization remains poorly understood. Using soils (Ferralic Cambisol) that had been collected from a long-term fertilization experiment for 23 years (1990 − 2013) in subtropic South China, we showed that soil organic carbon (SOC) stocks increased by 2.5 times following 23 years of manure fertilizations (pig manure or a combination of manure and chemical fertilizers) or by 1.4 − 1.8 times following non-manure fertilizations, compared to the initial SOC stock in 1990. Strikingly, soil bulk density after 23 years fertilizations decreased in the order: 1.41 g cm−3 (manure) > 1.26 g cm−3 (no fertilizer) > 1.12 g cm−3 (chemical fertilizer), suggesting that long-term manure fertilization increased soil bulk density when compared to the non-manure treatments. The X-ray micro-computed tomography further demonstrated that compared to the non-manure treatments, manure fertilizations decreased the number of pores, throats and paths as well as porosity. In addition, the stock of oxalate-extractable Al and Fe increased by 2 times following 23 years of manure fertilizations, relative to the initial soil. In summary, this study for the first time showed that changes in mineral reactivity impact soil physical properties and the potential of soils to stabilize C, strengthening the possibility in alleviating soil degradation and rebuilding a healthy soil.