Persistent overcast rain was an essential limiting factor for summer maize production, of which immediate impact was the dual pressure of waterlogging and shading. However, the mechanisms underlying independent and combined effects of waterlogging and shading on maize yield losses remain understudied, particularly across different growth stages. Denghai 605 (DH605) was selected to be subjected shading, waterlogging, and their combined stress at the 3rd leaf stage (V3), the 6th leaf stage (V6), and tasseling stage (VT). Results showed that shading, waterlogging and their combination significantly restricted leaf area expansion, reduced leaf net photosynthetic rate (P_n) and net assimilation rate (NAR), thereby decreasing the crop growth rate (CGR) and biomass accumulation. Additionally, compared to control, the process of lignin synthesis was inhibited under stressed treatment, resulting in diminished stem mechanical strength and impaired vascular system development, which substantially reduced assimilate remobilization efficiency to the ear and ultimate grain yield. Waterlogging and combined stresses exhibited maximum impact at the V3 stage, followed by V6 and VT stages, while shading effects were most pronounced at the VT stage, followed by V6 and V3 stages. Moreover, the compound stress exacerbated the damage brought about by a single stress. As climate change is projected to increase the frequency of multiple abiotic stress occurrences, these findings provide valuable insights for future summer maize breeding research under persistent rainfall conditions.