Relativistic magnetron is an important choice for high power microwave (HPM) source because it is relatively small compared with other HPM sources; in this respect, magnetron with diffraction output (MDO) is particularly attractive because its output port is already a horn. Previous experimental studies on MDO were conducted using a short pulse (~25 ns) SINUS-6 accelerator; here, we investigate the dynamical properties of an MDO under long pulse (~100 ns) and high monitored current (25–30 kA) conditions using a commercial particle-in-cell (PIC) code. The results show that MDO operation can be divided into two stages, and both are capable of HPM generation. At 450-kV applied voltage, the first stage happens between 0 and 35 ns when the transparent cathode rods emit electrons and they form spoke motion, and the dominant frequency is 4 GHz. The second stage happens after 35 ns, the spoke rotation in conventional magnetron region continues, but massive particles begin to flow toward the extended vanes region, and the dominant frequency is 2 GHz. If the applied voltage is higher, the stage transition happens sooner. Particle phase space plots show particle propagation toward the output port direction, which is a natural consequence of the pulsed power system and Lorentz force. Placing a cathode endcap on top of the cathode rods cannot stop the particles. The output power is well in the gigawatt (GW) realm and no pulse shortening is observed despite considerable particles are lost through contact with the anode wall in 100-ns pulse. The peak beam to microwave conversion efficiency is not as high as reported experimental value, but still a decent number close to 60%. Overall, the MDO is a suitable choice for certain applications that requires 100-ns pulse in GW range with high energy efficiency. [ABSTRACT FROM AUTHOR]