The field of advanced wastewater treatment, and more specifically, to a natural pyrrhotite biofilter and a method for utilizing same to synchronously remove nitrate-nitrogen and phosphorus from water is provided. The method includes the following steps: (1) preparation of the packing material and construction of the biofilter; (2) start-up of the biofilter; (3) operation of the biofilter. The method disclosed in the present invention on the one hand takes pyrrhotite as the electron donor to help sulfur-based autotrophic denitrifying bacteria reduce nitrates into nitrogen gas, and on the other hand utilizes pyrrhotite and its oxidates to eliminate phosphorus through adsorption and chemical precipitation. Therefore, this method realizes synchronous removal of nitrate-nitrogen and phosphorus in water.