DNA-modifying enzymes participate in various genetic functions (e.g., DNA replication, repairing, and recombination) through alternating certain DNA sequence, and the malfunction of DNA-modifying enzymes may disturb the normal genetic functions and consequently causes diverse human diseases. DNA-modifying enzymes may serve as the valuable diagnosis biomarkers and therapeutic targets, and the detection of DNA-modifying enzymes is essential to fundamental research, anticancer-drug discovery, and clinical diagnosis. Quantum dots (QDs) have many excellent electronic and optical characteristics, facilitating their biosensing and bioimaging applications. We review the development of QDs-based biosensors for DNA-modifying enzyme assays, and discuss current challenges and future directions in this field.