Graphdiyne (GDY) as an emerging two‐dimensional carbon allotrope exhibits excellent performance in energy chemistry, catalytic chemistry, optoelectronics, electronics, etc. because of the unique structure combining an sp‐ and sp2‐hybrid carbon network. However, the poor solubility of pristine GDY is a major obstacle to its applications in many fields. Proposed here is a facile strategy to control the preparation of GDY quantum dots (GDY‐Py QDs), in which pyrene groups are covalently linked to GDY by using a Sonogashira cross‐coupling reaction. The as‐prepared GDY‐Py QDs, with an average diameter of about 3±0.1 nm, show superior dispersibility in many organic solvents and water. The GDY‐Py QDs display not only bright fluorescent with a high relative quantum yield (QY) of 42.82 %, but they are also well‐behaved as contrast agents in cell imaging. The GDY‐Py QDs are bestowed with high stability and non‐cytotoxicity, and exhibit long fluorescent times, and have potential for optical imaging and biomedical applications.