The invention relates to the field of composite fertilizers, and in particular to a whole-element composite fertilizer and a preparation method thereof. The whole-element composite fertilizer consists of the following raw materials in parts by weight: urea, triple superphosphate, potassium sulfate, monoammonium phosphate, potassium chloride, ammonium molybdate, boric acid, polypeptide alkali chelate zinc, citrate chelate copper, long-lasting additives, illite powder, attapulgite powder and humic acid ammonium. The preparation method comprises the following steps: preparing pretreated raw materials, mixing and stirring, crushing cakes, pelletizing by using a pelletizer, drying granules, cooling the granules, screening, coating finished granules so as to obtain a finished product, and the like. The invention provides the whole-element composite fertilizer which is capable of effectively replenishing organic matters and various medium-trace elements which are urgently required by soil, improving soil structures, improving permeability, and promoting nutrient absorption of crops, and the invention further provides the reasonable preparation method for the whole-element composite fertilizer.