The invention discloses a pure natural multi-element organic fertilizer and a preparation method thereof. In the preparation method, the pure natural multi-element organic fertilizer is produced on a large scale by taking leftover furfural residues generated in a furfural plant, leftover spent mushroom compost generated by planting mushrooms, side product plant ash generated in a biomass generating plant and medicinal material dregs generated in a pharmaceutical factory as main raw materials, and adding an organic fertilizer fermenting agent for curing at a high temperature. The organic fertilizer produced by using the method has the advantages of high efficiency, low cost, high nutrition and stable quality, the problems of waste recovery, energy saving and emission reduction can be solved, soil biological balance can be improved simultaneously, and a series of agricultural problems such as soil hardening, salinization, acidification and the like caused by long-term use of a chemical fertilizer are solved. The technical indexes of the pure natural multi-element organic fertilizer produced by using the method are fully accordant with the requirements of more than or equal to 5 percent of nitrogen-phosphorus-potassium and more than or equal to 45 percent of organic matters in the novel organic fertilizer standard NY525-2012 implemented by the National Department of Agriculture in 2012.