Membrane proteins are the most abundant of whole proteome in mammalian cells and they play core roles in regulating cellular events. Membrane proteins also are good drug targets and it is important to monitor their dynamics and trafficking. Spectroscopic monitoring of proteins in living cells is a critical tool in cell biology as it allows non-destructive real-time observation of protein functions, interactions, and trafficking in their native context. However, as most proteins are not spectroscopically active it is desirable to introduce a spectroscopic tag to a target protein specifically in live cells. Here, we present a method to label membrane protein of interest based on split-intein mediated protein trans-splicing (PTS) reaction. A pair of engineered Npu DnaE were utilized for efficient labeling membrane protein on living cells. The labeling reaction occurred in two sequential reactions, namely via specific binding of two split-intein fragments followed by covalent conjugation through split-intein mediated PTS reaction. The specific binding occurred instantly and the covalent labeling was observed in 5 min on live cells with minimal background staining. This approach can be used as a tool to monitor the trafficking of membrane proteins and cell signaling events.