An inkjet printing system is provided, which includes a first stage mounted with a mother glass including a plurality of substrates and a plurality of alignment keys, a head unit having at least one inkjet head, an alignment key position sensor for sensing positions of the alignment keys to generate a plurality of sensing signals respectively corresponding to the alignment keys, and a transporting unit controller for aligning a position of the head unit based on a current position of the head unit and positions determined by the corresponding sensing signals with respect to the corresponding alignment keys.
