Lignin is the key component in the secondary cell wall of plants，which provides mechanical support and promotes water transport as well as has important impact responding to various biological and abiotic stresses. Averrhoa carambola L. is an important economic and ornamental species，the growing zone of which is restricted by its sensitivity to environmental stress conditions，such as strong wind，cold，and drought. However，lignin has significant impact on the improvement of stress resistance.To explore the lignin biosynthesis process of A. carambola L.，the issue microstructure was visualized using paraffin sections，and the changes of lignin content and enzyme activity were measured at different development stages of twigs. Bioinformatic analyses based on genome sequencing and transcriptome profiling were conducted to identify structural genes and transcription factors that associated to the lignin biosynthesis. The results showed that the increase on the activity of three enzymes（PAL，CAD and POD）and on the lignin content，as well as the appearance of xylem cells were observed along with the twigs development. A total of 41 structural genes，transcription factors（12 AcaMYBs and 11 AcaNACs）were identified in the A. carambola L. genome，followed by analyzing the differential expression patterns of these genes. The results of qRT-PCR found that AcaPAL1，AcaC3H2，AcaC4H2，AcaF5H1 and AcaMYB18 exhibit obvious tissue specific expression pattern，indicating these are specific genes related to lignin biosynthesis. Co-expression network analysis showed that AcaNAC29，AcaNAC39 and AcaMYB47were the essential regulatory genes of lignin biosynthesis. Collectively，this study provided important information to facilitate future research on the transcription factors and structural genes of lignin biosynthesis in A. carambola L..