In this paper, the TWTA (Traveling Wave Tube Amplifier) maintenance system for the low altitude surveillance Radar was developed using the embedded Linux system, and its superiority was demonstrated through the performance test. Nowadays, the necessity of maintenance system and reliability testing on military equipments has been increasing steadily. In addition, nonlinear characteristics of the maintenance system for the low altitude surveillance Radar are more likely to have serious problems as well as to slow down durability. Therefore, after analyzing characteristics of RF input-output signal and TWTA, we designed interface circuits between the TWTA equipment and the embedded Linux system. The Linux kernel on the system was optimized to improve the efficiency and reliability. And our new TWTA maintenance system was evaluated in the real field. As a result, the proposed system was contented with desired specifications, and demonstrated military's fighting capabilities. Therefore, our novel system will advance military maintenance technology and will help to develop similar equipments.