Short-term low-temperature stress during the flowering and boll-forming stages significantly inhibits cotton growth and yield. While leaf photosynthesis is a major contributor to cotton yield, non-leaf green tissues (bracts and bolls) also play a crucial role. However, the differential impacts of short-term low-temperature stress on the photosynthetic activity of these tissues and their protective mechanisms remain underexplored. In this study, the cotton cultivar "Xinluzao 45" was subjected to three temperature regimes in a controlled climate chamber: Control (30 degrees C/20 degrees C), T1 (16 degrees C/10 degrees C), and T2 (12 degrees C/8 degrees C). After two days of treatment, pigment content, photosynthetic activity, light energy distribution, and cyclic electron flow (CEF) around photosystem I were analyzed in both leaf and non-leaf green tissues. Results showed that short-term low-temperature stress decreased the maximum photochemical efficiency of PSII (Fv/Fm), actual photochemical efficiency [Y(II)], and maximum photo-oxidizable P700 (Pm) in both leaf and non-leaf green tissues. Compared to leaves and bracts, cotton boll shells exhibited greater photosynthetic stability, which was related to their higher carotenoid (Car) content, larger plastoquinone (PQ) pool, and enhanced CEF capacity under stress. Chemical inhibitor experiments (using antimycin A and rotenone) indicated that PGRL1/PGR5-mediated CEF plays a more critical role than the NDH pathway in cotton's response to short-term low-temperature stress. These findings highlight the distinct photoprotective advantages of cotton bolls and provide insights for breeding low-temperature-tolerant cultivars and improving management practices.