Objectives: The purposes of this study were to identify differently expressed microRNA (miRNA) after high-LET carbon ion irradiated human tongue squamous carcinoma Tca-8113 cells and to further study the microRNA roles in tumor radiotherapy.\r\n\r\nMethods: Total RNA was extracted from Tca-8113 cell after high-LET carbon ion irradiation. High throughput sequencing technique (HiSeq) was applied for detecting the differentially expressed genes (DEGs). The DEGs were divided into up-regulated and down-regulated genes. Flow cytometry was used for detecting the cell apoptosis; qRT-PCR was used for verifying the results of HiSeq. Via bioinformatic analysis, the distribution of candidate target genes and the significant enriched GO-term genes were obtained in the Gene Oncology (GO); With KEGG pathway enrichment analysis, the main signal pathways which DEGs take part in were obtained.\r\n\r\nResults: High-LET carbon ion irradiation induced the apoptosis of Tca-8113 cell and a total of 13 microRNAs expression changed. Three up-regulated (miR-40, miR-53, miR-643) and 10 down-regulated microRNAs (miR-278, miR-353, miR-31, miR-375, miR-106, miR-577, etc) were identified in Tca-8113 cells by HiSeq after high-LET carbon ion irradiation. Furthermore, the consequence of qRT-PCR was basically the same as the HiSeq. Via GO function analysis, there were 23 GO-terms in biological process, 18 GO-terms in molecular function and 20 GO-terms in cellular component and so 86 KEGG pathways enriched which DEGs take part in.\r\n\r\nConclusions: Our findings indicated that the high-LET carbon ion irradiation played a key role on microRNA expression of Tca-8113 cells and then these differentially expressed microRNA may become the potential molecular diagnostic biomarkers in tumor radiotherapy