A multilayer protruding embroidery process including the steps of laying and affixing a first filler on an embroidery background element; entirely wrapping up an embroidery portion of the first filler and the embroidering background element with a plurality of first sewing threads. Laying and affixing a second filler on the first and entirely wrapping up an embroidery portion including a side periphery of the second filler and background with a plurality of second embroidery threads. Fully cutting off and removing the leftover of the second embroidery portion and the first embroidery portion respectively, wherein said second portion is and outer portion of the second filler surrounding said embroidery portion, and the first embroidery portion is an outer portion of the first filler surrounding the first embroidery portion and thus a multilayer protruding embroidery is produced.