The invention discloses a submarine shallow-layer non-diagenetic natural gas hydrate lifting method and a system, which are used for lifting submarine shallow-layer non-diagenetic natural gas hydrate.A pilot hole is drilled by a drill bit, a pressure pump is started after a predetermined position is reached, high-pressure seawater drives a screw motor to rotate, and torque and rotational speed are transmitted to a screw pump by a cardan shaft; jet breaking is started by nozzles, hydrate is collected, secondarily broken and separated by collecting inlets, a secondary breaking device and a separator, separated sand is backfilled, and hydrate slurry is lifted to a solid control system on an offshore platform by the screw pump to undergo post-treatment. The invention has the following advantages: the whole process is simple, and submarine shallow-layer non-diagenetic hydrate can be effectively broken, separated and lifted; the screw pump device has the characteristics of compact structure, small size, high self-sucking capability, stable operation and long service life; and an upper bridge type passage and a lower bridge type passage ingeniously realize the pumping and lifting of seawater and hydrate slurry and save underground space.