This paper reports an integrated microfluidic system for single cell's refractive index measurement. In this system, a serial multiphase flow manipulation is proposed. Comparison to previous methods developed to measure the cell's refractive index in a microfluidic chip, it ensures that each cell is trapped inside a buffer plug and individually passes through the detection area. This method also avoids cell's wastage and measurement failure due to several cells gathered in the detection area. Results show that measured MDCK cells have an average effective refractive index of 1.383 ± 0.001.