Large 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. This work proposes two designed structures, called magnetic shields surrounding the anode and sputtering shields on the top of the inner and outer cathodes, respectively. The influence of the designed structure on the electromagnetic field and the plasma properties of the ion source are studied by a self-established simulation techniques based on the particle-in-cell/Monte Carlo collision method and test particle Monte Carlo method. The results show that the magnetic shields surrounding the anode cut off the magnetic induction line between the cathode and anode, which eliminates the arcing condition in the ion source. The sputtering shields for the cathodes use alumina ceramics because of the 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 directed to the output region for Ar ⁺ions, also resulting in a suppressed cathode etching behavior but an improved Ar ⁺ion output efficiency. The optimized calculation shows that the best distance from the sputtering shields 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. The detected Fe content, comes from the cathode sputtering, is only 0.03% after the plasma cleaning for 1 h, 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.