The invention provides a kilovolt (KV) control method and system adopting a digital technique. The KV control system comprises a KV closed-loop control system and a phase-shifting pulse-width modulation (PWM) signal generation module. The KV closed-loop control system comprises an outer ring and an inner ring, wherein the outer ring adopts KV closed-loop control, and the inner ring adopts inversion current effective value closed-loop control. The KV closed-loop control system and the phase-shifting PWM signal generation module are achieved through a field programmable gate array (FPGA) unit. The FPGA unit comprises a KV control main program module, an analog-to-digital (AD) conversion module, a KV control unit and a phase-shifting PWM signal generation module, wherein the four modules achieve KV double closed-loop control together. The KV closed-loop control mode includes: reading KV feedback values and inversion current effective values for once in each PWM period, and obtaining the pulse width values to be output in the next PWM period by adopting a proportional integral derivative (PID) control flow according to the deviation between KV reference values and the KV feedback values and the inversion current effective values. By means of the KV control method and system, the problem existed in a KV control circuit of a high voltage power supply simulation technique can be solved, and the KV closed-loop control effect is ensured to be in accordance with the KV closed-loop control effect of an analog circuit under the double-loop control condition.