The invention discloses a harmonic and inter-harmonic separation detecting method and device suitable for a vessel electric power system, and belongs to the technical field of vessel electrical engineering. The device comprises a voltage transducer, a current sensor, a chassis wiring terminal, a signal conditioning circuit, a data acquisition card and an industrial control computer, wherein the wiring terminal, the data acquisition card and the signal conditioning circuit are mounted inside the industrial control computer; the industrial control computer acquires input data through a standard serial port, and LabVIEW software of a virtual instrument is used for restoring collected signals according to the transformation ratio, and original signals are recorded; the comprehensive detection on parameters such as frequency, amplitude value and phase of fundamental wave, harmonic and inter-harmonic can be completed; the detection result can be directly displayed on the liquid crystal display of the industrial control computer. According to the invention, a frequency tracking algorithm, a fundamental wave and harmonic extraction algorithm and an inter-harmonic detection algorithm are adopted to implement the fundamental wave, harmonic and inter-harmonic separation detection.