Abstract Long-term spectroscopic monitoring campaigns on active galactic nuclei (AGNs) provide a wealth of information about its interior structure and kinematics. However, a number of the observations suffer from the contamination of second-order spectra (SOS) which will introduce some undesirable uncertainties at the red side of the spectra. In this paper, we test the effect of SOS and propose a method to correct it in the time domain spectroscopic data using the simultaneously observed comparison stars. Based on the reverberation mapping (RM) data of NGC 5548 in 2019, one of the most intensively monitored AGNs by the Lijiang 2.4 m telescope, we find that the scientific object, comparison star, and spectrophotometric standard star can jointly introduce up to ∼30% SOS for Grism 14. This irregular but smooth SOS significantly affects the flux density and profile of the emission line, while having little effect on the light curve. After applying our method to each spectrum, we find that the SOS can be corrected effectively. The deviation between corrected and intrinsic spectra is ∼2%, and the impact of SOS on time lag is very minor. This method makes it possible to obtain the Hα RM measurements from archival data provided that the spectral shape of the AGN under investigation does not have a large change.