MicroRNA (miRNA) chip and sequencing have been used to detect miRNAs in species. With the discovery of more miRNAs, miRNA target genes are the key to study miRNA biological function. Finding miRNA target genes mainly relies on computational prediction, AGO protein co-immunoprecipitation and luciferase. Deep sequencing, or degradome sequencing, can be used for high-throughput identification of targets of miRNAs. The method includes deep sequencing, bioinformatic analysis and 5'-rapid amplification of cDNA ends. It has been successfully used for global identification of miRNA-target RNA pairs in Arabidopsis thaliana, Oryza sativa and Physcomitrella patens. This paper reviews research progress in degradome sequencing in plant miRNA target study and discusses trends in further application of degradome sequencing.