In order to explore the gene expression pattern at transcriptional level of tomato after inoculated with Meloidogyne incognita， transcriptome sequencing was performed on tomato root at 6 h， 12 h， 24 h and 48 h after inoculated with 2nd instar larvae of root-knot nematode. The key transcription factor related to the tomato response to the infection of M. incognita were analyzed and the sequencing results were verified by quantitative real-time PCR. The results showed that 350， 390， 580， 1 154 genes were differentially expressed at 6 h， 12 h， 24 h and 48 h after inoculation， and 11， 11， 19 and 50 transcription factors were differentially expressed， respectively. They belonged to 15 transcription factor families， of which MYB family and bHLH family are the most abundant with 20 genes， followed by ERF family with 19 genes， WRKY family with 15 genes， and bZIP family with 9 genes. Further studies showed that the transcription factors of ERF，WRKY，MYB and bHLH family were the most differentially expressed. Solyc03g005520， Solyc02g094270 and Solyc09g066350 were significantly up regulated and the log₂FC at 48 h after inoculation was 9.16， 6.49 and 6.33， respectively. Solyc03g005520， Solyc02g094270 and Solyc09g066350 were significantly down regulated， and log₂FC at 48 h after inoculation was -2.60，-1.72 and -1.70，respectively. The results of qRT-PCR analysis showed that the expression trend of six randomly selected genes was consistent with the sequencing results. The results of this study suggest that the transcription factors of ERF， WRKY and bHLH family may be involved in the interaction between tomato and M. incognita， and play an important regulatory role in tomato response to the infection of M. incognita.