The invention discloses a method for improving the femtosecond laser processing accuracy. The method includes the steps that a measuring platform and a micro-nano structure processing platform are integrated, a sample distance detecting device and the rotation matrix method are combined, the position data of four to-be-processed areas is obtained through the detecting device and substituted into a rotation matrix, then calculation is carried out to obtain the corrected micro-nano structure position data, the data is substituted into a processing system, and the laser spot center is accurately positioned on a sample. The method has the advantages that switching between different platforms is not required, the surface height data is measured to be directly input to a computer, the errors caused by slopes of a to-be-processed sample, a substrate and the surface of a three-dimensional movable platform are eliminated with the rotation matrix method, the position of the processed sample is accurately positioned, the to-be-processed sample is accurately arranged at the center of a laser spot, the accuracy of laser micro-nano processing is further improved, the accuracy of femtosecond laser processing can reach about 300 nm accordingly, and it is guaranteed that the actual obtained structure and the preset structure are same.