Discloses is a vial automatic filling machine and a filling method thereof. The vial automatic filling machine comprises a conveying belt, a workbench, a portal frame, a screw rod sliding table, a lifting mechanism, a filling mechanism and a template. Locating equipment is arranged in a filling area. The advantages of precise filling and high filling speed are achieved. The equipment is used for achieving a dripping-free filling method, during filling, three stages of strokes are adopted, in the first stage of stroke, a movable plate drives an air cylinder to conduct driving, and thus a filling head directly stretches into a filling vial for filling; in the second stage of stroke, the movable plate drives the air cylinder to conduct driving, after filling, the filling head is driven to rise to a vial mouth to stay for a moment; and in the third stage of stroke, the movable plate drives the air cylinder to conduct driving, the filling head completely leaves the vial, and in this way, dripping leakage caused by the operation that after filling, a filling head directly leaves in the past is avoided. 3000 vials are filled hourly at most by a conventional filling machine, after the vialautomatic filling machine is adopted, 8000-15000 vials can be filled hourly, efficiency is improved by 2-5 times, and significant economic benefit is achieved.