Redesigned multifunctional biopolymers represent a novel building bridge for interdisciplinary collaborations in biomaterials development. We prepared fluorescein-grafted polyurethane scaffolds (PU-C1, PU-C5, and PU-B1) to meet both clinical needs and biological safety evaluations, using different contents of calcein and different synthesis procedures for potential biomedical tracing. X-ray diffraction, infrared, X-ray photoelectron spectroscopy, nuclear magnetic resonance, scanning electron microscopy, and light microscopy were used to analyze the composition and structure of polyurethanes, as well as to observe their morphology with and without biomarkers. Fluorescence spectrophotometer and fluorescence microscopy were used to detect the fluorescence characteristics. The results showed that the grafting of calcein significantly affected the chemical structure and fluorescence sensitivities of copolymers. When compared to calcein, which was added before synthesis (PU-C1), the marker that was added during the extender process (PU-B1) presented higher fluorescence efficiency. Both PU-C5 and PU-B1 exhibited strong fluorescent response and good cytocompatibility in vitro and in vivo, with no interference from the autofluorescence of tissues after 4 weeks of implantation. The fluorescence-marked material can be used to continuously and noninvasively monitor the dynamic changes in polymers, which provides a way to clearly trace the material or to distinguish between the material and tissue in vivo.