Large-scale green tides have occurred continuously in the Yellow Sea of China from 2007 to 2018, and the causative species of the Yellow Sea green tide (YSGT) is Ulva prolifera. The thalli form floated thallus mats, and the thalli from different layers of the thallus mat suffer significantly different environmental conditions. In the present study, the environmental conditions of the surface layer (SL), middle layer (ML), and lower layer (LL) of the thallus mat from mid-June (Stage I) to mid-July (Stage II) were simulated. Photosynthetic traits and antioxidant systems were measured. The results showed that (1) photoprotective [non-photochemical quenching (NPQ) and cyclic electron transport (CEF)] and antioxidant systems both play important roles in protecting against abiotic factors in U. prolifera. (2) Cooperation between NPQ and CEF was observed in the ML group; CEF and the antioxidant system in the SL group work synergistically to protect the thalli. Furthermore, an inferred spatiotemporal attribute regarding the YSGT is presented: the significant changes in abiotic factors on the sea surface can easily affect the thalli of SL and ML from mid-June to mid-July, and those of LL can be affected in mid-July. This cooperation combined with the spatiotemporal attributes offers an explanation for the annual occurrence of the YSGT.HIGHLIGHTS –Adaptive mechanisms of Ulva prolifera against abiotic factors. –Cooperation between photosynthetic and antioxidant systems. –Spatiotemporal attributes regarding the Yellow Sea green tide are presented.