A functional fertilizer composition containing natural mineral ingredients and a method of preparing the same are disclosed. More particularly, a functional fertilizer composition that is environmentally friendly, significantly accelerates growth of plants, relieves physiological disorders, is suitable for use as an agent for odor removal and a gas generation inhibitor, and enables preparation of a soil conditioner from a residue from which mineral ingredients are extracted and a method of preparing the same are disclosed. To this end, the method includes pulverizing vermiculite, mixing the pulverized vermiculite with water, adding sulfur or sulfuric acid to the mixture of pulverized vermiculite and water, stirring the mixture to which sulfur or sulfuric acid has been added, aging the stirred mixture to prepare an aqueous solution, and separating and extracting an aqueous solution containing mineral ingredients from the prepared aqueous solution.