The invention discloses a soil anammox bacterium gathering system simulating a natural environment, comprising a water intake tank, a peristaltic pump, a time controller, a reactor main body, a spray head, an earth pillar, a disc with holes, a support, a water discharging pipe, a precipitation zone, a sludge discharging pipe, a packing layer, a plurality of sludge taking ports, circular holes of the disc and circular holes of the spray head, wherein the lower part of the reactor main body is provided with the support, the reactor main body is sequentially provided with the spray head, the earth pillar, the disc with holes, the packing layer and the precipitation zone from top to bottom, the bottom of the reactor main body is provided with the water discharging pipe and the sludge discharging pipe, the sludge taking ports are arranged on the side wall for placing the earth pillar on the reactor main body, the upper end of the spray head is sequentially connected with the peristaltic pump and the water intake tank, and the peristaltic pump is connected with the time controller. The soil anammox bacterium gathering system has the advantages that an earth layer with the corresponding depth is put in the earth pillar to establish the earth pillar simulating the natural environment so as to be beneficial to the gathering of anammox bacteria in soil; the time controlling assembly realizes the intermittent water intake of the reactor; and the gathering system completely simulates the original ecology and can gather the anammox bacteria in a soil ecosystem.