Given that the nuclei studied in the nuclear physics experiments are expanding away from the stable nuclear region, traditional analog electronics acquisition systems can not satisfy the requirements of experiments that involve short-lived, low-yield nucleus productions under high background. In recent years, digital data acquisition systems have shown significant advantages over the analog electronics system and have been widely used in nuclear physics research such as studies of short-lived charged particle emitters which involve overlapping ion-particle or particle-particle signals, and studies of sub-microsecond isomers observed in fragmentation reactions. A general-purpose digital data acquisition system and a dedicated waveform analysis algorithm recently developed by the Group of Experimental Nuclear Physics, Peking University are introduced in this paper. This digital data acquisition system which is composed of 16-channel Digital Pulse Processor Pixie-16 modules from XIA LLC is a versatile, flexible, and expandable data acquisition system designed for nuclear physics research. Although the triggerless mode, which records all live events without event selection, provides an attractive option for users because it has great flexibility for offline data analysis, it also generates significant data streams in the experiments with high counting rates, which may then exceed the digital data acquisition system' I/O capability. Therefore, a flexible trigger system based on field programmable gate array has been developed to accommodate different experimental needs. The trigger system is configured through the hardware description language (VDHL/verilog), which can set up and debug different experiment logics conveniently. Many offline analysis tools have been developed to help users quickly optimize parameters for various types of detectors without time-consuming tests and measurements. Comparison between this digital data acquisition system and the conventional analog data acquisition system has been made. At low count rate, both systems exhibit good and comparable energy resolution. At high count rate above 8.8 k/s, while the energy resolution obtained by the analog system deteriorates significantly, the energy resolution obtained by the digital data acquisition system remains