The brain structure mismatch between western and eastern people may lead to an inappropriate interpretation of neurocognitive studies. To minimize this interracial misinterpretation, we developed the National Taiwan University Chinese Brain Template (NTU-CBT). 102 (M/F = 55/47) healthy Chinese subjects were recruited and received 3T MR brain scans. The template development processes were based on the construction process of Montreal Neurological Institute (MNI) template. Further pilot functional magnetic resonance imaging (fMRI) studies with blocked design visual stimulation and foot tapping task were performed on 3 volunteers and applied to both MNI template and NTU-CBT for analyses. 7 subjects were excluded due to motion artifacts. The average brain size of 95 (M/F = 50/45) subjects was 16.0 cm in length, 13.9 cm in width and 11.3 cm in height, which was 88.9%, 97.9% and 84.3% of the size of MNI template, respectively. Maximum dimensional differences came from the height of superior brain and the length of posterior brain. The average activation voxel volume of the fMRI studies applying to NTU-CBT was 80.7% of that to MNI template in visual stimulation, and 72.8% in foot tapping task. Noticeable mismatches were noted between interpolating original data to NTU-CBT and MNI template. Morphologic differences between MNI template and NTU-CBT do lead to spatial mismatch in functional studies, especially at cortical regions of superior and posterior brain. With the development of NTU-CBT, we look forward to more accurate interpretation in neurocognitive studies for Chinese subjects.