The invention belongs to the technical field of pollution monitoring. The invention discloses a system and a method for determining transfer of atmospheric settling heavy metals in sediments. The system for determining the transfer of atmospheric settling heavy metals in the sediments comprises a sample collection module, a deposition column preparation module, a seawater sample treatment module,an air sample treatment module, a soil sample treatment module, a first calculation module, a central control module, a bryophyte sample treatment module, a bryophyte sample analysis module, a secondcalculation module, a heavy metal transfer comparison module, a cloud storage module and a display module. According to the invention, atmospheric flow and disturbance of the external environment canbe isolated by utilizing the sediment seawater isolation method, the sediment is well protected, and a measurement result can accurately reflect a real numerical value of heavy metal from atmosphericsedimentation in the region; and the bryophyte is used as a biological monitoring indication plant, the atmospheric settlement heavy metal pollution condition is monitored by using a moss bag method,and basic data is provided for ecological environment protection.