Ataxia telangiectasia mutated and rad3-related kinase (ATR) and histone deacetylases (HDACs) are important therapeutic targets for cancer. In this study, a series of novel ATR/HDACs dual inhibitors containing 2-aminopyrazine motifs were designed and synthesized for the first time. Compounds 18b and 18c not only exhibited good dual inhibition activity against ATR (IC = 6 and 3 nM) and HDAC6 (IC = 6 and 20 nM), but also showed good anti-proliferative activity against four cancer cell lines. Preliminary mechanistic studies showed that compared with 18b, compound 18c exhibited stronger inhibitory effect on tumor cell proliferation and more effective induction of cell death. 18c could induce an increase in the level of acetylated α-tubulin and reduce the phosphorylation levels of ATR (p-ATR) and CHK1 (p-CHK1). Additionally, 18c also demonstrated the ability to upregulate the expression level of γ-H2AX. This research firstly presents the design and synthesis of ATR/HDAC6 dual-target inhibitors. The mechanism of action of these inhibitors may involve the synergistic induction of tumor cell apoptosis by dual inhibition of the DNA damage repair pathway and tubulin deacetylation processes. Overall, the research findings in this paper lay a foundation for further exploiting ATR/HDACs dual inhibitors' therapeutic usefulness while addressing potential drug resistance and adverse effect issues caused by combination therapy in clinical practice.