A digital accelerator (DA) is a low energy version of the induction synchrotron which has been demonstrated using the KEK 12 GeV-PS in 2006[1]. In the DA of injector-free, the acceleration and bunch confinement are independently carried out by induction cells, which are 1-to-1 transformers driven by individual switching power supplies. The switching power supply employing high power semiconductor switching devices (MOS-FET) can be operated at an arbitrary repetition rate up to 1 MHz with an output voltage of 2 kV. This characteristic allows us to realize a so-called all-ion accelerator [2] capable of accelerating all species of ion including cluster ions. To comply with specific demands for the induction acceleration in the KEK DA, that is a renovation of the existing KEK 500 MeV Booster synchrotron, a fully digital control system of the KEK DA is under development. It consists of high speed ADCs and FPGA (or DSP) to acquire the profile of beam bunch and process the required gate trigger signal from the profile data. It is crucial to trigger the acceleration system at the desired timing. Outline and R&D works of the control system described.