A method and device for eliminating narrow-band interference in spread spectrum system, wherein the method comprises the steps of: extracting N sampling points of the data to perform frequency spectrum transform each time and obtaining N points of data; getting the energy sum of individual data after M times of transform, obtaining N energy values, in which M≧1; removing partial excessive large values from N energy values and averaging the rest, then calculating the threshold value for interference determination based on the average value; obtaining the identification information of the points that have energy values exceeding the threshold value from N energy values and performing interference suppression for the data of corresponding points after frequency spectrum transform and finally outputting the data after frequency spectrum inverse transform. The device comprises a frequency spectrum transform unit, an interference elimination unit, an interference elimination control unit and a frequency spectrum inverse transform unit. The present invention could exactly distinguish interference data from non-interference data and effectively suppress narrow-band interference.