Telomeres localize at the ends of all linear chromosomes of eukaryotic cells to preserve genome integrity and cell survival. The highly repetitive telomeric sequences can easily fold into specific secondary structures that are difficult to replicate, resulting in increased replication stress. Telomeric repeats are bound by Shelterin complex, which consist of six telomere-specific proteins, and function to protect telomeres by preventing aberrant DNA damage response activation. Recently, it was shown that Shelterin components can also regulate the choice of DNA repair pathways in dysfunctional telomeres, and participate in telomere replication. In this review, we summarize how the secondary structures in telomere are stabilized/removed by Shelterin to ensure repilication proceeding. Moreover, we also discussed the inhibition of DNA repair at telomeres by Shelterin and how Shelterin mediates the repair pathway choice of dysfunctional telomeres. There is still much room to explore on the coordination between telomere protection, replication and regulation of telomeric DNA repair. Hopefully, the further exploration of telomere maintenance mechanism can provide new ideas and therapeutic strategies for telomere-related diseases such as aging and cancer.