The authors have built a 2 kW/28.5 kJ superconducting flywheel energy storage system (SFESS) with a radial‐type high‐temperature superconducting bearing (HTSB). Its 3D dynamic electromagnetic behaviours were investigated based on the H ‐method, showing the non‐uniform electromagnetic force due to unevenly distributed induced current may cause the superconducting magnet stator of the HTSB cracks. As the SFESS discharges, the amplitude and frequency of the discharge voltage decrease with speed, dropping by 55 and 58%, respectively, from the beginning phase (BP) to the middle phase (MP), by 41 and 37% from the MP to end phase. The decay rates of the discharge voltage and its fluctuation are both increased compared with the no‐load operation. During the BP to MP, the output power is higher, the power quality is better and the harmonics are less. The amplitude and frequency of radial vibration are proportional to speed, larger than that during the no‐load operation in the same case, and in the BP about 1.8 and 8.8% amplitude in the x and y directions, respectively. Its two norm is increasing by 2.6%, probably leading to the friction between the shaft and protective bearings, gradually becoming greater with speed.