Intensifying soil health means managing soils to enable sustainable crop production and improved environmental impact. This paper discusses soil health intensification by reviewing studies on the relationship between soil structure, soil organic matter (SOM), and ecosystem carbon budget. SOM is strongly involved in the development of soil structure, nutrient and water supply power, and acid buffering power, and is the most fundamental parameter for testing soil health. At the same time, SOM can be both a source and a sink for atmospheric carbon. A comparison of the ratio of soil organic carbon to clay content (SOC/Clay) is used as an indicator of soil structure status for soil health, and it has shown significantly lower values in cropland than in grassland and forest soils. This clearly shows that depletion of SOM leads to degradation of soil structure status. On the other hand, improving soil structure can lead to increasing soil carbon sequestration. Promoting soil carbon sequestration means making the net ecosystem carbon balance (NECB) positive. Furthermore, to mitigate climate change, it is necessary to aim for carbon sequestration that can improve the net greenhouse gas balance (NGB) by serving as a sink for greenhouse gases (GHG). The results of a manure application test in four managed grasslands on Andosols in Japan showed that it was necessary to apply more than 2.5 tC ha−1 y−1 of manure to avoid reduction and loss of SOC in the field. Furthermore, in order to offset the increase in GHG emissions due to N2O emissions from increased manure nitrogen input, it was necessary to apply more than 3.5 tC ha−1y−1 of manure. To intensify soil health, it is increasingly important to consider soil management with organic fertilizers that reduce chemical fertilizers without reducing yields.
