The inventive concept provides a method of manufacturing a semiconductor device using a plasma etching apparatus including an alignment chamber and a process chamber. The method includes: loading a wafer in the alignment chamber of the plasma etching apparatus; rotating the wafer loaded in the alignment chamber according to a plurality of heating zones arranged in an electrostatic chuck of the process chamber, thereby rotating a reference point of the wafer; transferring the wafer that was rotated in the alignment chamber onto the electrostatic chuck of the process chamber; and plasma-etching the wafer that was rotated in the alignment chamber on the electrostatic chuck of the process chamber.