Recently, some studies have established the ecological effects of intraspecific variation in phytochemical traits on soil ecosystems. Because plantations comprise a major proportion of forest area in some regions, intraspecific functional variation in plantation tree species is of great importance to forest ecosystems. Intraspecific variation in plantation tree species can result from natural geographical and cultivated variation. A previous study estimated the effects of geographical variation of Cryptomeria japonica, the most dominant plantation tree in Japan. The results showed that the significant consequences for ecosystem processes, such as calcium (Ca) dynamics and community composition of soil invertebrates, vary among the geographical variation of C. japonica. However, no studies have shown the effect of cultivar variation of tree species on the soil invertebrate community through alteration of the availability of nutrients. In this study, we used a common garden where four cultivars of C. japonica (Kumotoshi, Aya, Obi, and Satsumameasa) were planted in separate plots. In these plots, we measured the concentration of nutrients in leaves, litter and roots, strontium isotope ratio ( 87 Sr/ 86 Sr) of leaves. Root activities, exchangeable nutrients in soil, and soil parameters such as soil pH and abundance and composition of soil invertebrates. Our results show that cultivating different varieties of C. japonica may alter the accumulation of Ca in soil and soil pH. Furthermore, the effects of the cultivated varieties of C. japonica shape the abundance and composition of soil invertebrates by altering the soil properties, such as Ca concentration and pH in the soil.