During T lymphocyte development, immature T lymphocyte undergoes V(D)J rearrangement of T-cell receptor (TCR) genes to further develop to functional T cells. Upon this situation, additional DNA damage coming from the mutation of DNA replication genes sensitively makes immature T cells undergo apoptosis. While the mechanisms how immature T lymphocytes undergo fast cell death upon genomic instability have not been resolved. In our current study, we showed that in zebrafish mcm5 mutants, the immature T cells specifically and cell-autonomously undergo rapid apoptosis during T lymphocytes maturation. In mechanism, mcm5 loss of function results in DNA damage and up-regulation of tp53 signaling, sequentially gives rise to immature T lymphocytes apoptosis. Meanwhile upon mcm5 mutant, the absence of MCM5 decreases MCM5-Stat1 complex and disrupts phosphorylation of Stat1, which sequentially inhibits bcl2a transcription and accelerates the apoptosis of immature T lymphocytes. As the evidence, after blocking DNA synthesizing using chemical DNA synthesis inhibitors, MCM5 facilitates the up-regulation of bcl2a transcription to avoid rapid death of immature T lymphocytes. Our study first provides a mechanism as to how immature T cells with DNA damage coming from endogenous DNA replication stress are rapidly cleared off during early development, as well explains the extra biological role of MCM5 beside the role in DNA duplication regulation.