Astro-H is the sixth Japanese X-ray space observatory which will be launched in 2014. Two of onboard instruments of Astro-H, Hard X-ray Imager and Soft Gamma-ray Detector are surrounded by many number of large Bismuth Germanate (Bi4Ge3O12; BGO) scintillators. Optimum readout system of scintillation lights from these BGOs are essential to reduce the background signals and achieve high performance for main detectors because most of gamma-rays from out of field-of-view of main detectors or radio-isotopes produced inside them due to activation can be eliminated by anti-coincidence technique using BGO signals. We apply Avalanche Photo Diode (APD) for light sensor of these BGO detectors since their compactness and high quantum efficiency make it easy to design such large number of BGO detector system. For signal processing from APDs, digital filter and other trigger logics on the Field-Programmable Gate Array (FPGA) is used instead of discrete analog circuits due to limitation of circuit implementation area on spacecraft. For efficient observations, we have to achieve as low threshold of anti-coincidence signal as possible by utilizing the digital filtering. In addition, such anti-coincident signals should be sent to the main detector within 5μs to make it in time to veto the A–D conversion. Considering this requirement and constraint from logic size of FPGA, we adopt two types of filter, 8 delay taps filter with only 2 bit precision coefficient and 16 delay taps filter with 8 bit precision coefficient. The data after former simple filter provides anti-coincidence signal quickly in orbit, and the latter filter is used for detail analysis after the data is down-linked. ► We develop digital signal processing system of APD for Astro-H. ► We apply two types of digital filter instead of discrete analog circuit. ► By optimization, comparable or better energy threshold to analog shaper is archived. ► Developed digital filter works well in end-to-end performance test.