Saline-alkali land is one of the main land types for photovoltaic construction. In saline-alkali land photovoltaic system, the shading effect of photovoltaic modules affects soil water and salt dynamics by changing the microclimate, and crop growth is affected by both shading and soil salinity. The study of soil water and salt dynamics and physiological response of crops in saline-alkali land under shading has an important guiding significance for the development and utilization of saline-alkali land photovoltaic agriculture. In this study, Helianthus annuus Linn., a salt-tolerant and light-loving crop, was taken as the research object. The field experiment with four shading levels (0%, 30%, 60% and 90% shading) was designed to explore the effects of shading on the soil moisture content and soil salt content in 0-60 cm soil layer and the height, stem diameter, disc diameter, single leaf area, leaf photosynthetic gas exchange parameters, leaf photosynthetic pigment content, leaf photosynthetic enzyme activity, leaf anatomical structure, biomass, grain yield and grain quality of Helianthus annuus Linn. in coastal saline-alkali land, revealing the law of soil water and salt transport and crop growth and physiological changes in coastal saline-alkali land under shading. The results showed that the shading significantly increased the soil profile water content and decreased the soil profile salt content during the whole growth period of Helianthus annuus Linn. in coastal saline-alkali land. Shading decreased the net photosynthetic rate, inhibited the growth of stem and flower disc, decreased crude fat content and increased crude protein content of Helianthus annuus Linn. Under low light, Helianthus annuus Linn. promoted photosynthesis by increasing plant height, increasing leaf photosynthetic pigment content, decreasing leaf photosynthetic pigment ratio, increasing the enzyme activities of ribulose‐1,5‐diphosphate carboxylase (Rubisco) and phosphoenolpyruvate carboxylase (PEPC) in leaves, reducing leaf thickness, and changing the allocation direction of carbon assimilation product. At the shading rate of about 30%—60%, it was able to increase the soil water content of the tillage layer by 18%—38%, reduce the soil salt content of the tillage layer by 6%—18%, and maintain 15%—38% biomass and 29%—55% grain yield of Helianthus annuus Linn. The above results indicated that shading could improve the water and salt conditions of coastal saline-alkali land and alleviate the salt stress of crops, but Helianthus annuus Linn. as a light-loving crop, shading could inhibit its photosynthesis and affect its grain yield and quality. Therefore, it is recommended to plant Helianthus annuus Linn. in saline-alkali land photovoltaic system with the upper shading rate of photovoltaic modules of about 30%—60% to maintain grain yield.