The invention discloses a windowed Fourier transform-based stratum anomaly seismic detection method. The method comprises the following steps that: reflection wave lineups corresponding to a target layer are identified and tracked in a seismic section in a research area; the parameters of seismic trace signal Fourier transform of the research area are determined; a seismic trace corresponding to a normal stratum is selected as a standard trace, the ground vibration signals of the standard trace are denoted as f (t), and the frequency domain response F (omega) of the ground vibration signals is calculated; bell-shaped windows of which the center frequencies are omega1 and omega2 respectively are selected, and the frequency-domain response ratio Axi of the omega1 and omega2 is calculated; the frequency-domain response F'(omega) of the time-domain ground vibration signals f'(t) of non-standard seismic traces is calculated sequentially; bell-shaped windows of which the center frequencies are omega1 and omega2 respectively are selected, and the frequency-domain response ratio Bxi' of the omega1 and omega2 is calculated; and the percentage eta of the difference of the xi' and xi in the xi is calculated, wherein eta indicates the strength of the anomaly of a target stratum. The method has the advantages of scientificity, simplicity and quantitative and intuitive results.