Fluorescence imaging has currently emerged as one of the most frequently used noninvasive imaging technologies to selectively monitor biological processes in living systems. In past decades, gold nanoclusters (Au NCs) has received increasing attraction because of their intrinsic fluorescence and their inherent biocompatibility. As a stabilizing and reducing agent, an abundant, sustainable, and widely used polypeptide derived drug molecule, aprotinin (Ap), is selected for the synthesis of Au nanoclusters (Ap-Au NCs) due to characteristic bioactivity, excellent biocompatibility, biodegradability, and non-allergenic character. Herein, Ap encapsulated Au NCs with desirable red fluorescence was facilely produced for the first time, which were subsequently used for cell imaging and detection of various analytes. Much interestingly, dynamically subcellular targeting from the cytoplasm to the nucleus in HeLa cells was observed. Besides, it has shown that, the selective and quantitative detection of trypsin has been established by using Ap-Au NCs. Finally, Ap-Au NCs were readily used for quantitative detection of mercury and copper. The photoluminescence of the Ap-Au NCs was quenched with the addition of the aforementioned analytes. This study not only discusses a multifunctional nanomaterial for cell imaging, dynamically nuclear targeting and biosensing, but also opens crucial insights on the integration of funtional biomolecule with metal nanoclusters intended for extensively biomedical applications.