The blooms of coccolithophores are usually terminated by their viruses. However, little has been documented on the interplay between the host with virus under different environmental conditions. We investigated the relationship of Emiliania huxleyi (BOF92) and its virus (EhV99B1) after the coccolithophorid had acclimated to different levels of salinity (S35: 35‰; S25: 25‰) and CO₂ (AC: 400 μatm; HC: 1000 μatm) for about 15 generations. Our results showed that the virus infection decreased the growth of E. huxleyi along with decreased photochemical efficiency and photosynthetic carbon fixation under all the combinations of the treatments. Lowered salinity exacerbated the impacts of the viral infection on the growth and photosynthetic carbon fixation of E. huxley. The elevated pCO₂ appeared to have alleviated the impacts of the viral infection on its photosynthetic performance with enhanced levels of F_v/F_m, by about 49% under S35 and by about 16% under S25, respectively. Nevertheless, the elevated pCO₂ enhanced the virus burst size by about 18% under the high and by about 46% under the low levels of salinity, respectively. It is concluded that reduced salinity under the elevated pCO₂ exacerbates the impact of the virus on E. huxleyi, leading to the lowest algal cell density and the high burst sizes, and the enhanced photochemical efficiency and increased levels of Chl a under the elevated pCO₂ could have facilitated the energy supply for the reproduction of the virus in the infected E. huxleyi cells.