The invention relates to a biogas digester compressing gas through clear water. The biogas digester comprises a fermentation room, a gas storage room and a water pressure room which are connected withthe fermentation room is arranged on the upper part of the fermentation room, the top of the gas storage room is closed, the top of the water pressure room is opened, and the bottom of the gas storage room and the bottom of the water pressure room communicate; interlayers are arranged between the fermentation room and the gas storage room as well as between the fermentation room and the water pressure room correspondingly to form top covers, and the top of each top cover is made into a shape facilitating gas to be gathered together; the top of the interlayer at the gas storage room is openedand is connected with an inner gas collection pipe, the upper end of the inner gas collection pipe extends to the top of the gas storage room, the top of the of the gas storage room is opened and is connected with a gas supplying pipeline, the top of the interlayer at the water pressure room is opened and is connected with an outer gas collection pipe, and the other end of the outer gas collectionpipe is connected with the gas supplying pipeline; and the fermentation room is connected with a feeding pipe located below the interlayers, the interlayer at the water pressure room is further connected with a discharging pipe, and the bottom end of the discharging pipe is located below the interlayers. The problem that biogas generated by feces material liquid in a discharging room of a currentbiogas digester is directly vented, and consequently, not only are biogas resources wasted, and but also the environment is polluted is solved.