This paper reports the development of a high-throughput ZnO nanowire incorporated microdevice for microalgal cell transformation, in which the cellular attachment and detachment from the nanowires can be modulated through the operation of a pneumatic PDMS microvalve. We demonstrated superior nanowire-mediated gene transfer by tuning the pneumatic microvalve, and the target gene was inserted to microalgal cell with a high viability and gene integrity, which can provide an advanced genetic engineering tool.