Borehole thermal energy storage (BTES) is of great significance for improving energy utilization efficiency and achieving sustainable exploitation of renewable energy. However, the seasonal energy storage performance of BTES are affected by energy storage body parameters and their influence laws are still unclear. In this work, a 3-D numerical model of BTES is developed and validated by the model experiments. Effects of borehole spacing, borehole arrangement, soil stratification and groundwater seepage on the energy storage performance of BTES are numerically investigated. The results show that the energy storage body under different layout forms of borehole exhibits different temperature distributions and thermal diffusion characteristics, and the layout form 2 that the borehole spacing are 4.5, 3.5, and 2.5 m for the interior, middle, and exterior region borehole, respectively has obvious advantages during the energy storage. Compared with the uniform soil and the stratification soil 2 (the geological layers along the depth direction are respectively silty fine sandstone, fine sandstones, mudstone andstone), the stratification soil 1 (the geological layers along the depth direction are respectively sandstone, mudstone, fine sandstone, and silty fine sandstone) not only has larger heat storage and extraction amount, but also has larger energy storage efficiency. Compared to the sequential arrangement form, the staggered arrangement form provides a greater soil volume for energy storage. This leads to lower soil temperatures after heat storage and higher soil temperatures after heat extraction. Moreover, the staggered arrangement form results in larger overall heat storage and extraction capacities, as well as a greater heat storage amount per unit volume. The seepage is unfavorable to the seasonal energy storage of BTES, and the greater the seepage velocity, the more heat is carried to downstream by the seepage, causing heat loss and reduction of energy storage efficiency. Additionally, a small increase in the seepage angle can enhance the heat transfer effect of seepage, and thus the energy storage efficiency can be obviously improved.