The invention discloses a preparation method and applications of a biologically-fermented high-efficiency amino-acid-type organic enzyme preparation. The biologically-fermented high-efficiency amino-acid-type organic enzyme preparation is prepared via two times of biological fermentation of raw materials including kelp, plant raw materials, and fish meal. According to the preparation method, two times of fermentation is adopted, so that full utilization of the raw materials is realized, fermentation products are abundant, and contain main medium elements, micro elements, a plurality of amino acids, and enzymes which are necessary for plants. The biologically-fermented high-efficiency amino-acid-type organic enzyme preparation possesses high efficiency and obvious yield increasing effect on crops such as wheat, rice, cotton, soybean, peanut, oilseed rape, sugarbeet, and a plurality of vegetables and fruit trees, is green, is safe for crops, and is high in efficiency, the effect lasts long, no pollution is caused, and application cost is low.