The present invention relates to a sewage treatment system using granules, and more particularly, the sewage treatment system includes: an anoxic tank which has a sewage inlet port into which sewage is introduced; an anaerobic tank which is connected to the anoxic tank; intermittent aeration tanks which are connected to the anaerobic tank, have two or more separately divided spaces, and have, in the spaces, granules and aeration devices that alternately operate; and a settling tank which is connected to the intermittent aeration tanks, and the sewage treatment system is operated by a method including: a first step of introducing sewage; a second step of allowing the introduced sewage to pass through the anoxic tank and to be supplied with carbon; a third step of allowing the sewage passing through the anoxic tank to be introduced into the anaerobic tank; a fourth step of allowing the sewage passing through the anaerobic tank to be introduced into a first intermittent aeration tank and a second intermittent aeration tank which include the aeration devices and the granules including nitrogen treatment microorganisms; a fifth step of allowing the first intermittent aeration tank to be in an aeration state and the second intermittent aeration tank to be in a non-aeration state; and a sixth step of allowing the first intermittent aeration tank to be in the non-aeration state and the second intermittent aeration tank to be in the aeration state.