Abstract: Crop growth in saline photovoltaic systems is influenced by both soil salinity and shading. Understanding the physiological responses of crops under dual stress is crucial for guiding crop planting in this system. In a split-plot experiment with varying soil salinity levels (0, 3, and 5 g·kg⁻¹ NaCl, based on initial soil salt content) as the main zone and different shading levels (0%, 30%, 60%, and 90%) as the subzone, we investigated the effects of shading on the growth, photosynthetic characteristics, leaf anatomical structure, biomass accumulation, biomass distribution, and grain yield of Helianthus annuus L. under salt stress. This study provides a theoretical basis for crop cultivation in saline photovoltaic systems. The results revealed that shading, regardless of soil salt levels, compared with no shading treatment, disrupted photosynthetic reaction centers, reduced the light energy conversion efficiency of leaves, reduced the leaf thickness and palisade tissue layer thickness, inhibited the growth of the stem and flower disc, affected the accumulation and distribution direction of photosynthetic products, ultimately decreasing the grain yield of H. annuus. However, under moderate shade conditions, H. annuus showed improved light-capturing ability through increased plant height, leaf area, and enzyme activities of Rubisco and PEPC. Various shading levels, in comparison to the non-salt treatment, exerted additional effects under both mild and severe salt stress. These effects significantly impacted photosynthetic efficiency, inhibited plant height, stem, flower disc, and leaf growth, reduced the accumulation of photosynthetic products, and ultimately led to a reduction in the grain yield of H. annuus. The changes in the growth and photosynthetic physiological characteristics of H. annuus under different salt-stress concentrations were inconsistent across different shading levels. The 30% shading level significantly enhanced the enzyme activities of ribulose 1,5 diphosphate carboxylas (Rubisco) and phosphoenolpyruvate carboxylase (PEPC) in leaves, reduced leaf thickness, increased the palisade tissue layer thickness, and improved water use efficiency. Consequently, this enhancement led to improved photosynthetic efficiency and light energy conversion ability of H. annuus under slightly salt stress conditions. These results indicate that shading can inhibit the growth and photosynthetic efficiency of H. annuus under different salt levels, and H. annuus responds to environmental stress by changing its morphology, photosynthetic enzyme activity, and the direction of distribution of photosynthetic products in a low-light environment. Shading alleviated the negative effects of salt stress on H. annuus to a certain extent, in which the 30% shading level was more effective in alleviating the reduction in photosynthetic capacity and growth inhibition caused by slightly salt stress.