Non-photochemical quenching (NPQ) is one of the most important photo-protection mechanisms in brown macroalgae. Global warming and ocean acidification are predicted to impact physiological characteristics of marine algae. However, little is known about the effects of co-occurrence of the elevation of pCO₂ and temperature on photochemical capacity, especially regarding photoprotective mechanisms in brown macroalgae. Here, we studied the separate and combined effects of increases in pCO₂ and temperature on the photochemical characteristics and growth performance in sporophytes of the brown macroalga Saccharina japonica. The results showed that the NPQ of S. japonica is mainly dependent on the xanthophyll cycle (XC) which appears to be related only to the activation of the enzyme violaxanthin de-epoxidase (VDE), and the transthylakoid proton gradient (ΔpH) could not induce NPQ alone. The elevation of pCO₂ reduced NPQ value of S. japonica under high-temperature stress. After 60-day cultivation under the ambient and elevated pCO₂ (400 and 1000 μatm), we further found that the elevation of pCO₂ promoted growth and increased the photosynthetic performance of all three cultivar strains of S. japonica that have been traditionally cultured for many years in China.