This research proposed a new method for the determination of hexanal and heptanal by high performance liquid chromatography. Magnetic solid phase extraction coupled with in-situ derivatization was used as sample pretreatment method which occurred on the surface of the DNPH-adsorbed Fe3O4/SiO2/P(MAA-co-EGDMA). The sample pretreatment time of the proposed method was 9 min. Furthermore, the aldehyde derivatives obtained from the proposed MSPE-ISD method were stable, which simplified the determination of aldehyde and ensured the accuracy for quantification. The limits of detection (LODs) were 1.7 and 2.5 nmol/L for hexanal and heptanal, respectively. This proposed method can be applied to determine hexanal and heptanal in human urine from healthy persons and lung cancer patients that was simple, rapid and sensitive method.