Objective To describe a spatial coordinates conversion method for serial anatomical cross-sectional images of the human brain using the software, Excel 2003.Methods Initialization reference frame was established in serial anatomical cross-sectional images of the human brain. Then, a standard spatial coordinates was set up by one time horizontal moving and 3 times rotations of the reference frame. Results A datasheet about coordinates conversion from initialization reference frame to standard spatial coordinates was established. Conclusion Standard spatial coordinates was established in the digital human brain after coordinates conversion. It will be helpful to build Chinese digital brain model.