Abstract: Compared with relativistic magnetron with radial diffraction output, relativistic magnetron with axial diffractionoutput has series of advantages, such as compact structure, high impedance, azimuthal symmetry, steady mode and high output power.However, as the external magnet limits radius of axial output, lead to the axial length of the vacuum chamber is greater than the axiallength of the magnetron, a short transition section is designed for application. So the main task of this paper is to find appropriatetransition section through simulation, improving power transmission efficiency in S-band π-mode operating. The length of axialoutput section is 378 mm, the radius of cylindrical waveguide is 73.8 mm in output section. A effective transition section isachieved in three-dimensional particle-in-cell (PIC), power conversion efficiency can reach 28.7% corresponding to 1.371GW output and radiation mode is TE01.