Transcranial direct current stimulation (tDCS) is an emerging non-invasive neuromodulation method that is convenient and popular in clinical use. However, there is a practical issue in applying tDCS; it is difficult to optimize the montage for each individual because of inherent inter-subject variability. Thus, the stimulation effect of such individual anatomical head variation has been investigated using anatomically realistic models. In this work, we developed a multi-scale computational model, which combined head models based on magnetic resonance imaging (MRI) and multi-compartmental neuronal models of pyramidal neurons (PNs), to investigate both the macroscopic and microscopic effects oftDCS. We constructed three different head models and compared the stimulation effects of tDCS in the primary cortex area (Brodmann area 4) with respect to the electric fields induced and steady-state membrane polarizations. We observed that the electric field behavior and induced somatic polarizations varied across subjects in accordance with the thicknesses of cerebrospinal fluid (CSF) and skull measured in each model. Thus, we concluded that variations in the CSF and skull might be correlated with the effects of tDCS.