Under high light (HL) stress, astaxanthin-accumulating Haematococcus pluvialis and β-carotene-accumulating Dunaliella salina showed different responsive patterns. To elucidate cellular-regulating strategies photosynthetically and metabolically, thylakoid membrane proteins in H. pluvialis and D. salina were extracted and relatively quantified after 0 h, 24 h and 48 h of HL stress. Proteomic analysis showed that three subunits of the cytochrome b6/f complex were greatly reduced under HL stress in H. pluvialis, while they were increased in D. salina. Additionally, the major subunits of both photosystem (PS) II and PSI reaction center proteins were first reduced and subsequently recovered in H. pluvialis, while they were gradually reduced in D. salina. D. salina also showed a greater ability to function using the xanthophyll-cycle and the cyclic photosynthetic electron transfer pathway compared to H. pluvialis. We propose a reoriented and effective HL-responsive strategy in H. pluvialis, enabling it to acclimate under HL. The promising metabolic pathway described here contains a reorganized pentose phosphate pathway, Calvin cycle and glycolysis pathway participating in carbon sink formation under HL in H. pluvialis. Additionally, the efficient carbon reorientation strategy in H. pluvialis was verified by elevated extracellular carbon assimilation and rapid conversion into astaxanthin.