A method for manufacturing a panel having a surface of three-dimensional patterns and the structure thereof, first of all, provides a piece body, on the surface of which plane panel patterns are arranged by means of ink printing process, and which is thermally pressed into a plurality of projected three-dimensional panels. The piece body having projected three-dimensional panels is then placed between a lower mould and a first upper mould. A material of hard resin is injected into the clearance between the lower mould and the three-dimensional panel surfaces, and thus a transparent cladding layer capable of wear-resistance and protection for three-dimensional panels is formed. Next, material of hard resin is again injected into the space between the inner wall surfaces of the three-dimensional panels and a second upper mould for forming a supporting layer for supporting the three-dimensional panels. Afterwards, a material of rubber is injected into the space between a third upper mould and the inner wall surfaces of three-dimensional panels to form an elastic layer. At last, castings on the piece body and three molded layers are integrally cut according to respective contour to thus complete the manufacturing process of a single panel structure.