Accumulating evidences has been reported that long noncoding RNAs play crucial roles in the progression of hepatocellular carcinoma (HCC). snoRNA host gene 6 (SNHG6) is believed to be involved in several human cancers, but the specific molecular mechanism of SNHG6 in HCC is not well studied. Here, we found SNHG6 was highly expressed in HCC tissues. Next, using Hep3B and Huh7 cells, we confirmed knockdown of SNHG6 could reduce the proliferation, migration and invasion abilities in vitro. Also, by bioinformatics analysis, further molecular and cellular experiments, we found miR-6509-5p bound to SNHG6 directly, and the expression level of FKBP1A was regulated through SNHG6/ miR-6509-5p axis. Finally, we found that down-regulation of SNHG6 could dramatically reduce the tumor growth ability of Huh7 cells in vivo. Taking together, we concluded that SNHG6/miR-6509-5p/FKBP1A axis functioned in the progression of hepatocellular carcinoma, and could be the promising therapeutic targets in hepatocellular carcinoma.