In this paper, the method of applying cognitive radar technology to marine radar is studied, and the cognitive marine radar structure and transmitted signal model with three control parameters are constructed. The selection method of waveform control parameters, which is based on the target spatial distribution and the reference target detection effect with the minimum emission energy as the criterion, is given. The transmission signal control selection method given in this paper can flexibly realize different emission signal groups of m × n × p groups by independently setting the values m, n and p of three control parameters. It does not require radar hardware circuit reconstruction to meet the radar waveform changes. This is more convenient for the technical realization of cognitive marine radar. According to the method of this paper, a cognitive marine radar test system was constructed. The experimental results show that the proposed radar could reduce the emission energy by 15.9 dB compared with the traditional fixed-parameter pulse compression marine radar under the experimental conditions.