A new boundary prolongation method based on orthogonal polynomial fitting was developed to remove the signal-end effect. In the prolongation method M-order orthogonal polynomial was fitted with N points for both ends firstly,the low-frequency function of signal's both ends was expressed by orthogonal polynomial,and then the signal was extended with function,so the imported high-frequency parts were lowered. Results showed that choosing N from 30～50 and M from 2～4 was proper. Further experiment showed that the signal-end effect was cut down clearly when the method mentioned above was used in baseline correction with wavelet transformation.