Purpose <p>In the field of nuclear medicine and radiation therapy, Boron Neutron Capture Therapy (BNCT) is an emerging treatment method that can precisely kill cancer cells. It is a highly promising therapeutic approach. The design of the discharge chamber, a core component of the BNCT ECR ion source, directly impacts the performance and beam quality of the ion source.</p> Method <p>This article provides a detailed description of the design of the second BNCT accelerator ECR ion source (BNCT02 ECR) developed by the Institute of High-Energy Physics, Chinese Academy of Sciences. It mainly discusses the geometric structure, magnetic field configuration, and ridged waveguide structure of the discharge chamber, proposing two design options: a cylindrical discharge chamber and a square discharge chamber. Two designs aim to maximize the output beam current intensity, stability, and successful discharging of the ion source, along with experimental validation of the beam current.</p> Result <p>The issue of discharge instability caused by the positioning of ceramic blocks in the old discharge chamber has been solved. It is evident that the square discharge chamber exhibits lower reflection compared to the cylindrical discharge chamber, with a standing wave ratio (SWR) of only 1.06, and the SWR of cylindrical discharge chamber is 1.6. Taking the frequency at which the S11 curve decreases to − 3&#xa0;dB as the start and end points for bandwidth, the square discharge chamber’s bandwidth measures 19.674&#xa0;MHz, approximately 8.6 times that of the cylindrical discharge chamber’s bandwidth of 2.288&#xa0;MHz.</p> Conclusion <p>Square discharge chamber exhibits a broader operational bandwidth and a lower SWR and better discharging characteristics. Discharge chamber with wider bandwidth can help ion source adapt to frequency fluctuations, which fully improves the stability of the ion source. Low SWR design ensures easier discharging, guaranteeing the availability of the BNCT ECR ion source.</p>