The invention relates to an excavating harvester for long rhizome Chinese herbal medicines, in particular to an agricultural mechanical device for excavating and harvesting the long rhizome Chinese herbal medicines and belongs to the technical field of agricultural machinery. The excavating harvester for the long rhizome Chinese herbal medicines comprises a machine frame (1) and a gearbox (2). The excavating harvester for the long rhizome Chinese herbal medicines is characterized by further comprising an eccentric connecting rod excitation device (3), a secondary separating device (4) and a vibrating excavating separating device (6). The vibrating excavating separating device (6) is movably connected with the machine frame (1), the secondary separating device (4) is arranged at the back of the vibrating excavating separating device (6) and fixed on the machine frame (1), the vibrating excavating separating device (6) is hinged to the eccentric connecting rod excitation device (3) through a connecting rod (13), and the secondary separating device (4) is connected with an output shaft of the gearbox (2) through a transmission system.