The invention discloses a tissue chip making system based on image recognition and positioning and a chip making method thereof. The chip making system comprises a cutting system and a computer control system; the cutting system comprises a numerical control cutting machine, an XYZ axis translation work table, a 360-degree-rotation rotary table, a receptor wax block frame, a freezing table and animage recognition and positioning module. The chip making process of the chip making system comprises sample placing, sample position identification, tissue sample image acquisition, tissue sample image processing, setting of cutting parameters, cutting of a tissue sample, tissue chip information identification and storage, and obtaining of the tissue chip with traceability of information. The method obtains a chip taking area by visual identification, has the advantages of high degree of automation and high work efficiency, through linear cutting of the tissue sample, tissue damage is effectively reduced, and the chip taking efficiency and success rate are improved; a database is established for management of the information of the tissue chip, so as to be easy to follow-up queries.