The invention discloses a microsphere electric contact feedback insulating material workpiece surface alignment system and method. The alignment system comprises a micro-tool electrode, insulating liquid, a conducting microsphere, conducting liquid and an electric contact feedback system, wherein the micro-tool electrode serves as a carrier coated or dipped with the insulating liquid with the first preset volume and the conducting microsphere; the insulating liquid is used for enabling the micro-tool electrode to be bonded to the microsphere to realize automatic center alignment; the conducting microsphere is used for moving up when making contact with an insulating material workpiece to power on the conducting liquid and the micro-tool electrode to generate an electric contact signal; theconducting liquid is connected with one pole of a power supply and makes contact with the conducting microsphere and the micro-tool electrode to generate an electric contact signal; and the electriccontact feedback system is used for recording the current position of a contact point when detecting the electric contact signal and sending out a Z-axis feeding movement stop instruction. The microsphere electric contact feedback insulating material workpiece surface alignment system can realize accurate measurement on the height of the non-smooth non-conducting surface. Moreover, a measurement system is low in cost and easy to realize.