Genomic studies on hepatocellular carcinoma have revealed huge molecular heterogeneity of the cancer genome, which were closely associated with different pathobiology cancer progression. To unveil the transcriptomic heterogeneity including coding and noncoding RNAs, we performed profiling of mRNA and micro RNA sequencing from the hepatocellular carcinomas and non-tumoral surrounding tissues. Molecular clustering analysis identified two subtypes with distinct expression of mRNAs and noncoding RNAs, which were significantly associated with patients' clinical outcomes. Differentially mutated genes between the subtypes were also found, which included previously well-known cancer driver genes such as CTNNB1 and NOTCH2. MicroRNA profiling demonstrated the subtypes enriched with the expression of microRNA clusters located in chromosome 14 and 19, which have close interactions with transcriptome aberrations. In addition, long noncoding RNA transcripts and a novel fusion transcript were found, which can promote cancer progression. Our analysis provide a comprehensive landscape of coding and noncoding transcriptome variations in hepatocellular carcinoma, providing new insights on the pathobiology of heterogeneous liver cancer progression.