A manufacturing method of micro channel structure is disclosed and includes steps of: providing a substrate; depositing and etching to form a first insulation layer; depositing and etching to form a supporting layer; depositing and etching to form a valve layer; depositing and etching to form a second insulation layer; depositing and etching to form a vibration layer, a lower electrode layer and a piezoelectric actuating layer; providing a photoresist layer and depositing and etching to form a plurality of bonding pads; depositing and etching to from a mask layer; etching to form a first chamber; and etching to form a second chamber.