Waterlogging during the anthesis, exacerbated by continuous rainy weather and heavy soil, has become a primary limiting factor affecting wheat yield in southern China's rice‐wheat rotation regions. Previous research indicates that utilizing exogenous 6‐benzylaminopurine (6‐BA) can effectively alleviate the adverse effects of continuous rain on wheat yield, while the fundamental process is yet to be fully understood. In this research, two wheat varieties with contrasting waterlogging sensitivities were selected, which were exposed to waterlogging and shading for 7, 11, and 15 days after anthesis. Subsequently, three different concentrations of 6‐BA solution (15, 25, and 35 mg L−1) were applied through spraying. The application of 6‐BA significantly increased the total soluble sugar and starch content in grains during the filling process, as well as enhanced the activities of starch synthesis‐related enzymes: sucrose synthase (SuS, EC 2.4.1.13), ADP‐glucose pyrophosphorylase (AGPase, EC 2.7.7.21), and starch phosphorylase (Pho, EC 2.4.1.1). Moreover, the application of 6‐BA notably enhanced the transfer and transport rate for non‐structural carbohydrates (NSC) in the stem and sheath. It resulted in a notable increase in the distribution ratio of dry matter in the grain, ultimately leading to higher grain weight and yield. Applying 6‐BA through spraying mitigated the adverse effects of waterlogging and shading on starch accumulation and dry matter transport in grains, thereby improving grain weight. The most effective concentration in this experiment was 25 mg L−1.