The invention discloses a chromatographic baseline noise reduction method. The method comprises the following steps: S1, signal acquisition, S2, signal amplification, S3, Gaussian noise removal, S4, impulse noise removal, S5, calibration fitting and S6, component analysis. A SG filter is connected with a morphological filter in series so that the advantages of the SG filter and the morphological filter are integrated, while the defects of the SG filter and the morphological filter are eliminated, Gaussian noise is removed through the SG least square filtering algorithm, and then impulse noiseis removed through the morphological filtering algorithm. The method has the advantages that most of noise is removed through the SG least square filter, and the amplification effect of the morphological filter on the noise is avoided; and then the morphological filter is used to filter the problem of residual abnormal point interference of the SG filter. The sequence of the two steps cannot be reversed, otherwise, the defects of the two algorithms are amplified. Fnally, the two filtering algorithms in the invention are real-time algorithms, the acquired signals can be filtered in real time,and the delay is within 0.5 s.