Anterior gradient protein 2 homolog (AGR) is a potential tumor biomarker and plays an important role in tissue development and regeneration. The intracellular detection of AGR is rarely reported. By conjugating the AGR aptamer with a cytosine base sequence as Ag cluster template, a highly fluorescent probe (MA@AgNCs) was synthesized for targeting intracellular AGR. The MA@AgNCs display a maximum fluorescence peak at 565 nm, and possess an excellent quantum yield (QY = 87.43 parts per thousand), small size, great biocompatibility, low toxicity, and good stability. Moreover, the as synthesized MA@AgNCs show high specificity on recognizing breast cancer cells.