The invention discloses a harmonic rapid analysis method and system based on windowing four-spectral-line interpolation FFT, and relates to the field of harmonic analysis. The method comprises the following steps: signal preprocessing; the determining of four spectral lines; the calculation of a modifier formula of a four-spectral-line interpolation algorithm; the calculation of a fundamental wave parameter; the performing of a four-spectral-line interpolation rapid algorithm; the determining of a harmonic parameter; and error analysis. The method starts with a frequency domain expression of a windowed power grid signal of a power system, and a phase rule among the four biggest spectral lines adjacent a real spectral line point after windowing FFT is deduced according to the rule of a phase different pi between any two adjacent spectral lines in a main lobe of a window function. The invention proposes a windowing four-spectral-line interpolation FFT rapid algorithm. Compared with two-spectral-line and three-spectral-line interpolation algorithms, the method provided by the invention effectively improves the precision of harmonic analysis. The method just needs one modular operation for a harmonic wave at a certain order, can effectively reduce the calculation amount and time, and remarkably increases the calculation speed.