Stump–root systems consist of aboveground stumps and underground coarse roots after timber harvesting. Stump–root systems are the primary source of coarse woody debris (CWD) in plantations, and they play a crucial role in the material cycle, energy flow, and biodiversity of Eucalyptus plantation ecosystems. However, there is limited knowledge about the changes in elemental stock within this CWD type during decomposition. To address this gap, we conducted a study on Eucalyptus urophylla × E. grandis stump–root systems at various times (0, 1, 2, 3, 4, 5, and 6 years) after clearcutting. Our aim was to investigate the stock changes in eight elements (K, Ca, Mg, S, Fe, Mn, Cu, and Zn) within the stumps and coarse roots over time and their decay levels, and we analyzed the relationship between elemental stocks and the physical, chemical, and structural components of stump–root systems. Our findings revealed the following: (1) The majority of each element’s stock within the stump–root system was found in the coarse roots. The elemental stocks in both stumps and coarse roots decreased as time passed after clearcutting and as decay progressed. (2) Notably, the elemental stocks in stumps and coarse roots were significantly higher than in other treatments during the initial 0–2 years after clearcutting and at decay classes I and II. In terms of elemental stocks, stumps from all clearcutting times or decay classes had the highest K stock, followed by Ca and Fe. Mg, Mn, and S stocks were lower than the first three, while Zn and Cu stocks were very low. The ordering of elemental stocks from high to low in the stump–root systems generally aligned with that of the coarse roots. (3) The residual rates of K, Mg, and Mn stocks in the stump–root systems fit the negative exponential model well. It took approximately 1 to 3.5 years for a 50% loss of the initial stocks of these elements and 5 to 10 years for a 95% loss. (4) The large amount of biomass in the stump–root system is the long-term nutrient reservoir of plantations, and any factor related to biomass loss affects the magnitude and duration of the nutrient reservoir, such as N, P, stoichiometric ratios, density, water-holding capacity, and hemicellulose. These findings contribute to a better understanding of the nutrient elemental dynamics and ecological functions of stump–root systems in Eucalyptus plantations.