Abstract: A new full-digital power supply measurement system was designed to achieve better measurement accuracy, improved noise suppression, and lower cost. In the proposed system, four kinds of data are sent from digital power supply regulator via an optical interface with a frequency of 2 kHz. A set of high-performance digital signal acquisition equipment receives, time-stamps and stores data of each power supply. Data analysis graphical user interface was provided. Actual use of the system indicates that it fulfills design requirements. Digital measurement is firstly applied in power supply system of heavy ion medical accelerator. It can be popularized in future heavy ion accelerator based on its strong anti-interference and economy.