Frequency stabilization for external cavity diode laser has played an important role in physics research. Many laser frequency locking solutions have been proposed by researchers. Traditionally, the locking process was accomplished by analog system, which has fast feedback control response speed. However, analog system is susceptible to the effects of environment. In order to improve the automation level and reliability of the frequency stabilization system, we take a grating-feedback external cavity diode laser as the laser source and set up a digital frequency stabilization system based on National Instrument’s FPGA (NI FPGA). The system consists of a saturated absorption frequency stabilization of beam path, a differential photoelectric detector, a NI FPGA board and a host computer. Many functions, such as piezoelectric transducer (PZT) sweeping, atomic saturation absorption signal acquisition, signal peak identification, error signal obtaining and laser PZT voltage feedback controlling, are totally completed by LabVIEW FPGA program. Compared with the analog system, the system built by the logic gate circuits, performs stable and reliable. User interface programmed by LabVIEW is friendly. Besides, benefited from the characteristics of reconfiguration, the LabVIEW program is good at transplanting in other NI FPGA boards. Most of all, the system periodically checks the error signal. Once the abnormal error signal is detected, FPGA will restart frequency stabilization process without manual control. Through detecting the fluctuation of error signal of the atomic saturation absorption spectrum line in the frequency locking state, we can infer that the laser frequency stability can reach 1MHz.