High beam-anode layer ion source can produce high-density ions, and has been widely used in plasma cleaning and assisted deposition. However, when increasing the ion-beams, arcing always occurs inside the ion source and serious etching will take place on the cathode, which results in sample pollution especially in long-time cleaning. In this work, two structures are designed, which are magnetic shielding around the anode and sputtering shielding on the top of the inner cathode and outer cathode, respectively. Based on the particle-in-cell/Monte Carlo collision method and test particle Monte Carlo method, the influence of designed structure on the electromagnetic field and the plasma properties of the ion source are studied through self-established simulation technique. The results show that the magnetic shielding around the anode cuts off the magnetic induction line between the cathode and anode, eliminating the arcing condition in the ion source. The sputtering shielding for the cathode uses alumina ceramic because of its extremely low sputtering yield and high insulation performance. Therefore, the sputtering shields can not only resist the ion sputtering, but also shield the electric field on the outer surface of the cathode. As a result, the plasma discharge region is compressed towards the anode and away from the cathode simultaneously, which provides a stronger electric field force directing to the output region for Ar<sup>+</sup> ions, and also results in a suppressed cathode etching behavior but an improved Ar<sup>+</sup> ion output efficiency. The optimized calculation shows that the best distance from the sputtering shield to the cathode surface is 9 mm. The discharge experiments reveal that the modified ion source can eliminate the inside arcing and provide a clean and strong ion beam with a high efficiency. At the same discharge current, the output efficiency of the modified ion source is 36% higher than that of the original ion source. When used in the plasma cleaning, the glass substrate remains transparent and keeps the original element composition ratio unchanged. The detected Fe content, coming from the cathode sputtering, is only 0.03% after the one-hour plasma cleaning, which is 2 orders of magnitude smaller than that cleaned by the original ion source. The Fe content of the modified ion source is about 0.6% of the original ion source, which is in good agreement with the result of simulation optimization.
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