The present invention relates to a method for preparing a composition for fruit tree flower pruning using natural hormones and a use method of a composition prepared thereby, wherein the composition, which utilizes natural growth control hormones in seaweed and particular plant growth control materials, is scattered at a particular time when fruit trees flower to a predetermined degree or completely, thereby giving a favorable flow pruning effect whereby the falling of flowers is induced to control the rate of growth of fruits, and the composition helps the growth of fruits and the growth of leaves and stems, necrotizes only flower tissues, and causes no disturbance in the growth of leaves, stems, and fruits, thereby bearing only good fruits in large quantities. The composition for fruit tree flower pruning using natural hormones in the present invention helps the development of fruits and the growth of leaves and stems and necrotizes only flower tissues, thereby causing no disturbance in the growth of leaves