The invention discloses a method for synchronously removing heavy metals and nitrates in mine wastewater and a reactor. The method comprises the following steps: sludge enrichment and domestication, preparation of a biological agent, preparation of a double-layer iron-carbon filler, biofilm formation and operation of the reactor. The reactor comprises a double-layer iron-carbon filler, a gas washing plate, a guide plate, a supporting layer, an outlet aeration system and a filter plate from top to bottom, a backwash valve is arranged at the bottom of the reactor, a backwash water tank controls the flow through a backwash flowmeter, and a water inlet pump pumps water to cooperate with a gas washing plate to realize backwash; two exhaust holes are formed in the top of the reactor; and water is discharged from the water outlet and then enters a sedimentation tank for sedimentation and drainage. A double-layer iron-carbon filler is adopted, nitrate is removed under the effect of microorganisms, microorganism precipitates (FeOOH, Fe2O3 and Fe (OH) 3) are generated to adsorb and remove Cd < 2 + >, Pb < 2 + > and Ni < 2 + >, and the method has the advantages of being free of secondary pollution, high in biological activity, low in cost, easy to operate and manage and the like.