The maize variety 344 was used as the experimental material, and the physiological characteristics data and the transcriptome differential gene expression data of maize seedlings under low phosphorus stress were analyzed. To deciphers the molecular regulation of physiological changes in maize Leaves under low phosphorus stress, and preliminarily identified the key genes involved in physiological response under low phosphorus stress. The results showed that under low phosphorus stress, chlorophyll fluorescence parameters (FV/FM) and chlorophyll content of maize leaves decreased in varying degrees, chlorophyll synthesis related genes were mostly down-regulated, and chlorophyll degradation related genes were mostly up-regulated. Most of the genes related to photosynthetic characteristics of maize leaves were down-regulated, and photosynthetic efficiency was significantly reduced. Under phosphorus stress, the activities of SOD and POD increased gradually with the increase of treatment time, and most of the genes encoding the two enzymes were up-regulated. At the same time, eight key genes of MDA synthesis LOX were detected，and seven of them were up-regulated under phosphorus stress. Meanwhile, the content of MDA increased gradually during low phosphorus treatment.