Background Betatrons are widely used in non-destructive testing, cargo and vehicle security inspection systems, whilst the filament power supply is an important core component of small size betatron. Existing filament power supplies are not suitable for small size betatron. Purpose This study aims to develop a novel electron gun filament power supply for small size betatron to produce optimal radiation intensity. Methods An electron gun filament power supply composed of a filament duty cycle adjustment circuit and an injection current feedback circuit were designed on the basis of operating characteristics of a small size betatron. Two pulse-width modulation (PWM) signals were output from the digital signal processor (DSP) to drive the half-bridge circuit. Positive and negative alternating voltage pulses were output by the half-bridge circuit to the primary of the isolation transformer, and the secondary voltage of the transformer was loaded to the filament for heating of the filament. By collecting the betatron tube wall current and target current as the injection current feedback signal, the duty cycle of the filament voltage pulse was adjusted by DSP according to the feedback signal, and realizes the adjustment of the filament emission current, so that the current injected by the filament into the acceleration tube was kept at the optimal value. Results The experimental test results show that the filament power supply can keep the betatron output dose rate in the best state, and the output dose rate stability is better than 11.3%/10 min. Conclusions The filament power supply meets the requirements of small size betatron with advantages of good stability, wide adjustment range and small size. It can be applied to the small size betatron developed by the Engineering Research Center for Nuclear Technology Application of the Ministry of Education of East China University of Technology.