Soils in plantations of Cryptomeria japonica in Japan have ~threefold more exchangeable Ca compared with soils in other types of forest vegetation even in a Ca-poor environment. To explain mechanisms underlying this phenomenon, we determined the effect of root exudation rate of low-molecular-mass organic acids (LMMOAs) on exchangeable cations in soil. We conducted a pot experiment using C. japonica and five dominant tree species in Japan, and measured the root exudation rates of LMMOAs and exchangeable nutrient concentrations in the soils. To estimate whether the root exudation rate of LMMOAs is elevated in response to Ca deficiency, we created variation in Ca availability by adding different amounts of crushed oyster shells. The root exudation rates of LMMOAs were two to five times higher for C. japonica than for other tree species, but did not differ significantly among the different quantities of oyster shell. Exchangeable Ca and Mg were significantly higher in the soils with C. japonica and significantly correlated with the root exudation rate of LMMOAs (R² > 0.24) at high and moderate quantities of oyster shell. Therefore, variation among species, in terms of root exudation of organic acids, might be one important factor affecting the cation dynamics in soil.