Tomato plants are easily infected by pests and fungi, which seriously influences the yield and quality. The objective of the present study was to determine the effect of five types of nitrogen (N) treatments on volatile organic compounds (VOCs) by determining the changes in the transcriptome levels of genes related to phenylalanine metabolism, amino acid biosynthesis and plant-pathogen interaction as well as VOCcontent in tomato leaf during growth. The results indicated that low N treatment (1/20 N and 1/5 N) promoted the production of VOCs compared to high N treatment (2 N and 3 N). Low N treatment enhanced the levels of α-pinene, camphene, β-ocimene, D-limonene, caryophyllene, humulene, terpineol, carveol, (E)-2-hexanal, methylis salicylas and cyclobutene. Low N treatment upregulated the differentially expressed genes (DEGs) involved in phenylalanine metabolism and amino acid biosynthesis, which may influence peroxidase, 4-coumarate-CoA ligase, 4-hydroxyphenylpyruvate dioxygenase, caffeoyl-CoA O-methyltransferase, tyrosine aminotransferase, glycine hydroxymethyltransferase, anthranilate phosphoribosyltransferase, branched-chain amino acid aminotransferase, pyruvate kinase (PK), fructose-bisphosphate aldolase, and other enzymes. These enzymes could increase the synthesis of VOCs. Additonally, the DEGs in plant-pathogen interaction have a significant down-regulated trend in 2 N and 3 N compared with 1/20 N, which also responsed the low N could enhance the defense capacity in tomato. In summary, Transcriptome data showed that low N could promote the up-regulation of volatile substances related genes and the increase of VOCs verified the above changes in transcriptome data. Meanwhile, the change of gene in plant-pathogen interaction also demonstrate low N can enhance the defense capacity during tomato growth.