The invention discloses a copper-based ultra-thin heat pipe with a super-hydrophobic-super-hydrophilic structure and a preparation method. The preparation method includes the steps that a copper baseplate is milled to form a groove face and is cleaned thoroughly; a first area of the groove face is subjected to face scanning through a nanosecond laser processing device, a continuous capillary structure with a fuzzy morphology is formed, and a super-hydrophobic area is obtained after heat treatment; after the copper base plate is cooled, a second area of the groove face is subjected to face scanning through the nanosecond laser processing device, a continuous capillary structure with a fuzzy morphology is formed, and a super-hydrophilic area is obtained; two copper bases in the same size and with continuous capillary structures are welded together in a manner that the groove faces are opposite; and after work media are injected into a cavity formed by the two groove faces, sealing treatment is performed. According to the copper-based ultra-thin heat pipe with the super-hydrophobic-super-hydrophilic structure and the preparation method, due to laser surface modification, and the manner that the super-hydrophobic areas and the super-hydrophilic areas of the continuous capillary structures are alternately distributed on the inner wall, the heat dissipating efficiency is substantially improved, and the heat pipe is lighter and thinner.