Abstract: In this work, we designed an FPGA-based digital anti-coincidence gamma-ray spectrometer system to reduce the effect of the natural background radiation and Compton scattering on detection of the low-level radioactivity. In this system, the anti-coincidence detector consists of a NaI(Tl) detector with a size of Φ75 mm×75 mm and an annular NaI(Tl) detector (Φ145 mm×95 mm×80 mm), the FPGA and the ADC were employed to sample the pulse signal from the main detector and the annular NaI(Tl) detector synchronously. We designed the related algorithms running in FPGA, such as signal acquisition and caching, anti-coincidence discrimination, and trapezoidal shaping. In the natural background measurement, the digital anti-coincidence gamma-ray spectrometer system reached a count rate of 191.80 cps and a suppression of background radiation coefficient of 2.69. In the ¹³⁷Cs source irradiation experiment at the center of the front face of the anti-coincidence detector, the peak to total ratio reaches 0.41 and the energy resolution is 6.99%. The peak to total ratio reaches 0.30 and the energy resolution is 7.48% when the ¹³⁷Cs source is placed in the middle part of the anti-coincidence detector. The experimental results show that the FPGA-based digital anti-coincidence gamma-ray spectrometer system in this paper can reduce the influence of natural background radiation and Compton scattering effectively, and can be used for on-site radioactivity detection and low-level radioactivity measurements.