The Korea Atomic Energy Research Institute (KAERI) has used a microtron accelerator based on a thermionic cathode for operating a compact terahertz (THz) FEL, where the electrons are emitted and accelerated automatically during the radio-frequency (RF) macro-pulse over threshold power for their emission. Usually a thermionic cathode is embedded inside the microtron cavity for electron-beam emission, and at the same time acceleration is due to the input RF source. In this case, the accelerator scheme is simple, but just a fraction of the emitted electrons are accelerated, and the electron bunch length is uncontrollable due to the RF phase condition for acceleration. In this paper, a photocathode-based microtron which is able to produce high peak (∼100 A) and ultrashort (∼1 ps) electron bunch is studied to adapt it for an electron injector of a THz generator. Especially, we analyzed the electron beam dynamics along the accelerating trajectory with a 3D PIC-code to find the optimized RF phase and laser input time.