The invention provides a multi-cabin silt sampler and a sampling method thereof. The sampler comprises a rocking arm, a plurality of sampling cups, a valve disc, a valve seat, a step motor and a central shaft, wherein the sampling cups are uniformly distributed on the valve seat along the circumference; the valve disc is provided with a plurality of sampling components and a plurality of through holes, which are corresponding to the sampling cups one by one; the sampling components comprise valve rods, elastic parts and sealing gaskets; the sealing gaskets are arranged below the plurality of through holes, and can seal the through holes; the sampler is also provided with a separation component; the separation component is connected with the valve seat and the valve disc, and can regulate a distance between the valve disc and the valve seat. According to the multi-cabin silt sampler, a structure that the sampling cups are uniformly distributed along the circumference is adopted; the rocking arm is controlled through the motor to compress and open the valve rods to inject water; the sealing is achieved by spring mechanical return; thus, the collection of a plurality of water samples can be automatically and continuously completed; the efficiency is improved; through the design of the central shaft, a chassis, a ring nut and a lifting nut, the valve disc can be conveniently separated from all the sampling cups and the operation efficiency is high.