Trehalose protects and stabilizes the reaction center and improves photosystem II (PS II) activity. However, the underlying mechanism remains unknown. Cyclic electron flow is an important mechanism to protect PS II under stress. This study focused on the effects of exogenous trehalose on the activity of PS II, D1 protein content, the plastoquinone (PQ) pool, and ATP synthase activity in wheat seedlings under heat and drought stress to explore the relationship between trehalose and cyclic electron flow (CEF). Our experimental results indicated that heat and drought stress decreased the maximal photochemical efficiency of PS II (Fv/Fm) and the electron transport rate of PS II (EFR(II)), whereas the trehalose pretreatment improved photochemical efficiency and the electron transport rate of PS II. The trehalose pretreatment stimulated CEF under heat and drought stress. Furthermore, the proton gradient (ΔpH) across the thylakoid membrane and ATPase activity increased. The higher ΔpH and ATPase activity played a key role in protecting PS II under stress. Inhibition of the oxidized PQ pool caused by heat and drought stress was alleviated by the trehalose pretreatment. Thus, our results show that photoinhibition of heat and drought-stressed plants was alleviated by the trehalose pretreatment. Our findings further reveal that this effect was mediated by CEF and the PQ pool.