The invention relates to sea sampling equipment, in particular to a high throughput deep sea water sampling and graded filtering system. The system comprises a mounting rack, and a filter device, a fixed clamp, a flowmeter, a control and power supply device and an integrated deep sea pump separately mounted on the mounting rack; the filter device comprises an upper cover, a flow guide mechanism, atensioning mechanism, a bottom tray, multistage filter membranes and a supporting net. The flow guide mechanism and the multistage filter membranes as well as the supporting net are located between an upper cover and the bottom tray and are connected through the tensioning mechanism to form a closed cavity; a water inlet communicating to a water outlet of the integrated deep sea pump is formed inthe upper cover, and a water outlet communicating to the flowmeter is formed in the bottom tray; the control and power supply device is connected to the integrated deep sea pump through a water density cable; the filter membranes are arranged on the filter device, so that graded filtration is achieved; the integrated deep sea pump can work in deep water in situ. The system can carry out high throughput in-situ graded filtration in deep sea, and has the advantages of being ship time-saving, acquiring samples in situ and the like.