Atherosclerosis (AthS) tends to form at arterial regions exposed to disturbed (DF) but not laminar (LF) flow. Previously, we reported the significant role of SUMOylation in DF-induced endothelial (EC) activation and subsequent AthS formation via upregulating p53 and ERK5 SUMOylation. LF can inhibit the basal levels of p53 and ERK5 SUMOylation, but how LF inhibits SUMOylation remains unknown. A chemical genetics approach with high-resolution mass spectrometry revealed that the cell-cycle checkpoint kinases CHK1 can phosphorylate SENP2 S344 site, but the functional role remains largely unknown. We aimed to study the functional role of CHK1 in SENP2 function and subsequent AthS. First, we generated phospho-specific SENP2 S344 antibody, and found that LF, but not DF, increases SENP2 S344 phosphorylation. We found the increase of CHK1 S280 phosphorylation (related to nuclear translocation) after LF, suggesting LF-induced nuclear translocation of CHK1. The CHK1 specific inhibitor of GDC0575 and the depletion of CHK1 inhibited LF-induced SENP2 S344 phsophorylation and increased both p53 and ERK5 SUMOylation in ECs. These data suggested the crucial role of CHK1 in LF-induced SENP2 S344 phosphorylation and upregulating de-SUMOylation activity. Next, we generated CRISPR/Cas9-induced Senp2 S344A knock-in (KI) and found that the mutation of SENP2 S344A accelerated p53 and ERK5 SUMOylation. LF-induced reduction of p21, cleaved caspase 3, and ICAM-1 were all reversed by SENP2 S344A mutation. Lastly, we found that the significant acceleration of AthS formation in both ascending aorta/arch (DF area) and descending aorta (LF area) in KI mice compared to wild type (WT) mice after receiving AAV-PCSK9 and high fat diet. We also performed bone marrow transplantation (BMT) after 13 Gy whole body radiation, and larger AthS but only in the aortic arch was observed in BMT mice from WT donor to KI recipient, but not in BMT mice from WT donor to WT recipient, supporting the role of endothelial SENP2 S344 phosphorylation on AthS. The radiation reduced CHK1 expression in ECs, which may explain the different regulatory pattern under BMT or non-BMT. Taken together, these results suggest the critical role of CHK1-mediated SENP2 S344 phosphorylation on LF-induced anti-AthS effects.