The invention belongs to the field of aviation composite material part manufacturing, and particularly relates to a positioning and punching method for a composite material honeycomb sandwich part packing area. The size of small-diameter through holes, part of a composite honeycomb sandwich part, is 50 mm or less, a line drawing positioning is easy to be caused positioning deviation, so that a filling padding needs to be reworked after the part is drilled. According to the positioning and punching method for the composite material honeycomb sandwich part packing area, a conical pin is arrangedat the theoretical punching position of a tool, and only the conical part is exposed, and a veneering surface prepreg is laid on a molded surface of the tool, and then the convex veneering surface prepreg is cut off according to the conical part; a honeycomb sandwich layer is placed, and a packing is filled with the conical part as a center; a non-veneering surface prepreg is laid, the whole transfer is carried out, heating and pressurization solidification are carried out; and drilling is carried out according to conical holes formed in the bottom. The positioning difficulty of the packing area in the part manufacturing process is reduced, the position precision of the packing area is improved, the reworking repair rate is reduced, and the product quality is improved.