As the gold standard for stealth polymer materials, poly(ethylene glycol) (PEG) has been widely used in drug delivery with excellent properties such as low toxicity, reduced immunogenicity, good water solubility, and so forth. However, lack of understanding for the fate of PEG and PEGylated delivery systems at the cellular level has limited the application of PEGylated molecules in diagnosis and therapy. Here, we chose linear PEG 5k as a representative model and focused on the internalization behavior and mechanism, intracellular trafficking, sub-cellular localization, and cellular exocytosis of PEG and PEGylated molecules in living cells. Our investigation showed that PEG could be internalized into cells in 1 h. The internalized PEG was localized to lysosome, cytosol, endoplasmic reticulum (ER) and mitochondria. Importantly, the fate of PEG in cells could be regulated by conjugating different small molecules. PEGylated rhodamine B (PEG-RB) as the positively charged macromolecule was internalized into cells by micropinocytosis and then transported in lysosomes, ER, and mitochondria via vesicles sequentially. In contrast, PEGylated pyropheophorbide-a (PEG-PPa) as the negatively charged macromolecule was internalized into cells and transported to lysosomes ultimately. PEGylation slowed down the exocytosis process of RB and PPa and significantly prolonged their residence time inside the cells. These findings improve the understanding of how PEG and PEGylated molecules interact with the biological system at cellular and sub-cellular levels, which is of significance to rational PEGylation design for drug delivery.