In this study the cucumber and wheat plants were used to clarify the mechanism of redroot pigweed’s allelopathic effects on photosynthesis. In order to reach that goal, plants were cultivated hydroponically, treated by redroot pigweed’s leachate and finally chlorophyll fluorescence and photosynthetic gas exchange parameters, photosynthetic pigments content and the expression of photosynthetic genes (PsbA and PsbS) and allelochemical interaction with proteins of studied genes were analyzed. After exposure to the allelopathic stress, significant differences in the majority of photosynthetic characteristic were observed in the studied species. Redroot pigweed allelopathy led to alteration in photosynthesis performance, photochemistry, and photosynthetic genes expression of cucumber and wheat plants, ultimately its results were observed in morphological traits of plants. Molecular docking study strongly confirmed the possibility of direct binding and action of allelopathic compounds with allelopathic action’s target proteins. Overall, this study showed that compared to cucumber, the wheat plant is able to withstand the damaging effects of amaranth allelopathy on photosynthesis in order to resist and survive.