The present invention relates to an immersion hollow fibrous membrane separating device and the operation method thereof. The device comprises a membrane filtration system, a water producing system and a cleaning system which are connected by the tubes and a control system which is connected by a circuit, the present invention is characterized in that the membrane filtration system takes an immersion type, adopting a column external pressure hollow fibrous membrane component, a plurality of holes are arranged at the casing, the device is directly and vertically arranged in the processed water body; the water producing system comprises a pressure gauge, an automatic intake valve, a water producing pump, a flow meter and an automatic discharge valve which are sequentially connected with a water producing opening of the membrane module; the cleaning system comprises a backflushing system, a gas vacuole scrubbing system and a chemical cleaning system, the gas vacuole scrubbing system comprises a flow meter, an air inlet valve, an air adjusting valve, a filtrating pressure reducing valve, an air receiver and an air compressed valve which are sequentially connected with the backflushing air intake of the membrane module. The operation method includes a plurality of cyclic processes as follows: 1. an operating state, a backflushing state, a gas vacuole scrubbing state and a pollution discharge state; 2. the operating state, the backflushing and gas vacuole scrubbing state, an gas vacuole scrubbing state and the pollution discharge state; 3. the operating state, a chemical backflushing state, the gas vacuole scrubbing state and the pollution discharge state.