Abstract: We addressed the mechanisms responsible for the major problems, including but not limited to the instable oscillation-starting, low mainlobe-to-sidelobe ratio, ineffective suppression of interference, intra-pulse and inter-pulse frequency-shifting, frequent sparks and short service life-time, of the lab-developed S-band high power pulsed magnetron, operating at 2.6 MW and to be used in particle accelerator.The influence of the modified structures, improved fabrication techniques and optimized operation conditions on the characteristics of the magnetron was theoretically analyzed, numerically simulated and experimentally evaluated.The prototyped magnetron, fabricated on the basis of optimization of design/fabrication/operation-conditions, was tested.The results show that the total solutions we proposed here work pretty well.For instance, when it comes to frequency spectrum and reliability, the newly-designed magnetron meets the application requirements.