The present invention relates to a manufacturing method of puzzle shape drawing cookies. In particular, more specifically, the design of cookies which express a fairy tale or a piece of a picture in a story is worked with a computer CAD program; a single sheet of paste kneaded in a flat shape of a constant size is covered with a plastic, and is then transferred to a CAM cutter; the paste can be cut in a puzzle shape, in which the cross-section is a straight line, a circle or a curve, according to a cookie shape designed with the CAD program; drawing story cookies are cut using the CAM cutter, thereby providing convenience; and cookies with stories are formed and expressed such that cookies are made to create events according to the nature of individual countries, thereby improving profitability. In addition, a piece of a drawing story is created as a cookie, thereby bringing about a revolutionary change in the confectionery industry; when the top of a cookie is colored after the cut paste is baked in an oven and created as a cookie form, a mixture in which natural fruit powder, natural vegetable powder and some pigments are added to icing sugar, egg whites, and concentrated lemon juice is placed and worked in a nozzle duct, thereby enabling drawings to have different kinds of flavors and appearances; and flower paste is made with a mixture in which natural fruit powder, natural vegetable powder and some pigments are added, such that different types of shapes are expressed on and attached to the top of the baked cookie, and then, by using an automated machine system, it is possible to easily imprint shapes and attach the same to the top of a cookie in a short time when expressing different shaped petals, leaves, stems, and forms of various objects on the top of a cookie as drawings. Furthermore, by using a nozzle duct, which is an automated machine system, it is possible to easily coat the top of a cookie which has been molded, cut and baked, with color drawings havi