This study aimed to clarify the environmental factors limiting the height of aged Cryptomeria japonica trees. The study was conducted on C. japonica plantations of about 100 years old at the Boso Peninsula, Japan, where the climatic conditions are almost uniform. Twenty-eight plots measuring 10 × 10 m were established on ridges, and 40 plots were established on the middle or lower sections of slopes. The stand ages ranged from 93 to 115 years old. The height of the tallest tree and soil depth (SD) were measured in each plot, and the wetness index (WI) and openness (OP) of each plot were calculated using a digital elevation model. The tree height at the 100-year age (H100) was estimated. The H100 ranged from 16.2 to 44.9 m and was significantly correlated with the logWI (r = 0.78) and OP (r = −0.70). SD and H100 were significantly correlated in the plots on the ridges but not in the plots on the middle or lower sections of slopes. It indicated that soil water retention capacity might limit tree height in the relatively dry soil conditions. The coefficient of determination adjusted by the number of parameters for H100 predicted using multiple regression analysis with environmental factors of logWI, logWI and OP, or logWI, OP and SD were 0.60, 0.69, and 0.73, respectively. The inclusion of OP and SD in the model improved the prediction of H100, suggesting that the wind and rooting depth could be the influencing factors in determining the height of aged trees. The findings of this study could be used in the planning and management of forestry plantations of long rotation system.