The invention discloses a bioreactor for efficiently and economically synchronously removing nitrate nitrogen and ammonia nitrogen. A water distribution area, from bottom to top, is sequentially provided with a sludge discharge pipe and a water return-inlet pipe, a transverse partition plate is respectively arranged between the upper end of a short-range denitrification area and the bottom of an anaerobic ammonia oxidation area and between the upper end of the anaerobic ammonia oxidation area and the bottom of a separation area, the upper end of the short-range denitrification area and the bottom of the anaerobic ammonia oxidation area, as well as the upper end of the anaerobic ammonia oxidation area and the bottom of the separation area, are respectively connected through a flange, the two transverse partition plates are respectively provided with a sludge guide pipe and a liquid guide pipe, the upper part of the short-range denitrification area and the upper part of the anaerobic ammonia oxidation part are respectively provided with a gas pulse tube, the short-range denitrification area and the anaerobic ammonia oxidation area are respectively filled with a ball packing layer, the side wall of the separation area, from bottom to top, is sequentially provided with a sludge discharge outlet, an overflow tank and a water outlet, the center of the separation area is provided with a double-effect three-phase separator, the side wall of the middle part of the double-effect three-phase separator is provided with a return pipe, and the upper part of the double-effect three-phase separator is provided with a gas collecting connecting pipe and a gas exhaust pipe. According to the invention, an effect of simultaneous denitrification and carbon removal is achieved without aeration; due to the adoption of pulse exhaust, the floating loss of sludge is controlled; because the double-effect three-phase separator is provided, gas, liquid and solid phases are effectively separated.