Laser manipulation system combining microfluidic and microimaging devices was developed, in which a cell sorting in a transparent microchip was successfully demonstrated. The microchip containing two microchambers was prepared with laser microfabrication, in which a solution containing yeast cells was injected as a sample. In the microchip, a cell transfer from one chamber to another one was performed by using single, fixed trapping laser beam. Furthermore, to realize an efficient cell sorting, the trapping laser beam was split into two by a polarizing beam splitter and each beam was modulated independently; one trapping beam was used to trap individual cells and to move them, which is freely controlled by a mouse pointer, and another was used to store the selected yeast cells with its liner scanning. In this method, the cells on a locus of the scanned beam were isolated to transfer in the microchip. From these results, it is concluded that shortening of the cell sorting time in microchip by a few time was realized by using dual-beam laser manipulation.