In order to testify the algorithms for the detection of wake targets in sea clutter background, a navigation radar signal acquisition and analysis system is developed. The system uses USB2.0 as the interface of microcomputer and works with FPGA as its kernel chip. Experimental results show that it can satisfy the data acquisition and analysis tasks of the navigation radar. The system can record and store the original information for later processing, to analysize the various characteristics of targets and clutter. It provides the basis for radar signal processing and target detection algorithm.