The goal of this work is to design and fabricate an autonomous acoustic recording system which is low cost, reconfigurable and portable for acoustic research. The system consists of four components, including a compact single-board computer (Celeron 1G), a 12-bit A/D converter (PCM-3718HO), a 20/40 dB gain amplifier and an useful power management circuit board. C and LabVIEW programs with multiple threads are developed to control the I/O's, digitize the underwater acoustic signals and stream data to the hard disk continuously. Currently, the throughput of data stream attains to 83 kHz. It were tested by six significant experiments to show its feasibility. At first, taking the function generator as signal source to verify no distortion caused by the system. Two ITC-6050C hydrophones are connected to the system as the receivers. The system was tested with experimental propeller producing broadband noise to calibrate the hydrophones in the experimental sink. To verify their performance, the receivers also work with the calibrated one B & K 8104 for reference. In order to understand the influence of self-noise, the system is planned to record known signal producing by hydrophone CTG-0708. By repeating similar calibration experiment, the system operates with an autonomous recording system Bioacoustic probe to understand what deficiency we should improve afterward. Further, a field test was conducted in the designated natural laboratory of shallow bay area. Post-processing of the data resulted in range-frequency plot shows that the interference pattern reported in the literature was captured. According to above-mentioned tesing, the system can be applied to underwater acoustics. This system, connected with multiple hydrophones, will be applied in the research for target detection, the harbor protection and so on.