Phaeodactylum tricornutum is model organism for marine diatom. It is also one of the most popular energy microalgae. The genome sequence of P. tricornutum had been completed. But, the gene function analysis and gene regulation research of P. tricornutum need further exploration. In this paper, we constructed the glycerol kinase gene knockout vector for P. tricornutum, and successfully converted the vector to wild type P. tricornutum by particle bombardment. After screened, 34 transformations were obtained. The analysis of cell growth showed that extracellular glycerin had no effect on the cell growth of the transformats. Detected by western blot, the results presented that the expression of glycerol kinase were repressed or reduced in transformants. In short, we explored a knockout system for further gene function research in P. tricornutum.