The invention provides a seismic data surface wave removing method based on adaptive sparse S transform. The seismic data surface wave removing method comprises the steps of: acquiring a time-frequency map from seismic records, and determining a region in which surface waves to be suppressed locate in the time-frequency map; performing spectral analysis on the selected region in which the surface waves locate, and determining a corresponding frequency range; subjecting a seismic trace to adaptive sparse S transform along a t axis, and transforming the seismic trace into a t-f-x domain; subjecting the transformed data to Fourier transform along an x axis, and transforming the data into a t-f-k domain; filtering a seismic signal in the t-f-k domain by using a mask function M(f, k); performing inverse Fourier transform and inverse S transform on a filtered result, and returning to a time domain to obtain a result of the data of the seismic trace after surface wave denoising; and processing data of all traces accordingly to obtain seismic data after removing the surface waves. The seismic data surface wave removing method can effectively separate the surface waves from effective information in the transform domain, thereby effectively removing the surface waves in the seismic data and improving a signal-to-noise ratio of the seismic data.