The invention discloses a rural sewage advanced treatment and biochemical filtration integration device and a running method thereof. The device is provided with a sewage equalizing tank, a sewage pretreatment tank, a biochemical pool, a biochemical filter tank, a discharged water tank and an equipment room, the sewage equalizing tank is provided with a water discharge pump and is connected with the sewage pretreatment tank and the biochemical tank; the biochemical tank is provided with an overflow hole, and is connected with the biochemical filter tank; the bottom of the biochemical tank is provided with a sludge discharge pump, the bottom of each of the biochemical tank and the biochemical filter tank is provided with an aerating pipeline connected with a blower and an aerating head, and a filter membrane and a back flush pump are arranged in the biochemical filter tank; and the device is also provided with a control board connected with the above pumps and the fan. The running method comprises the steps of water feeding, aeration of the biochemical tank, precipitation of the biochemical tank, feeding of water to the biochemical tank and aeration of the filter tank, aeration of the biochemical tank, precipitation of the biochemical tank, sludge discharge of the biochemical tank, and back flushing of the biochemical filter tank. The device is suitable for rural sewage treatment, has the advantages of simple operation, unmanned operation and low cost, and realizes advanced nitrogen and phosphorus removal of the rural sewage.