Stem cell regenerative medicine strategy requires selecting functional cells to trigger repair processes. Stem cell secretion measurement is important to evaluate cellular activities for functional cell sorting. At present, to determine single cell secretions, mixing chemical sensors and cells together in a chamber is a standard procedure. However, toxic chemical sensors, such as albumin assay kits, are used during this process, causing low viability (64%) and low functionality (30%). It is especially important for stem cell profiling, as the toxicity of chemical sensors such as albumin permanently changes stem cell phenotypes, leading to unwanted analysis outcomes. Moreover, because of the sensor toxicity, the challenge of culturing sorted cells remain. In this study, an integrative synchronized droplet screen system was developed to separate a large droplet with cell encapsulation into two daughter droplets: one droplet containing cell secretions and the other droplet containing a single cell. These two daughter droplets moved along the channels at the same speed in synchronization. By injecting toxic chemical sensors into one daughter droplet, the single-cell secretions were determined without affecting the cells in the corresponding droplet. Based on the daughter droplet synchronization, the cells without mixing toxicity sensors were sorted for cell culturing. For example, to identify hepatocytes, the albumin secretion of undifferentiated HepaRG stem cells was measured in daughter droplets by injecting a toxic albumin assay kit for functional stem cell sorting. With synchronized sorting, functional hepatocytes were collected without exposure to toxic chemical sensors, showing high viability (78%) and active functionality (89%).