Two kinds of culture systems were constructed, namely, an artificial substrate system (novel sponge biocarrier, SB) and a water exchange system (WE), to evaluate the effects of the microalga Haematococcus pluvialis on the water quality and performance of whiteleg shrimp (Litopenaeus vannamei). The results showed that the average NH₄⁺-N concentration with H. pluvialis was lower than those without it. The average concentration of NO₂^?-N and NO₃^?-N in SB system were significantly decreased than those present in WE system, but there was no significant difference in SB system. The growth performance of shrimp with H. pluvialis was superior to that without it. The final average weight and growth rate of shrimp in SB1 and WE1 tanks were differed significantly among that present in SB2 and WE2 tanks (p?<?0.05). SB1 tended to have the highest average weight gain and lowest feed conversion ratio. The shrimp survival was significantly higher in SB1 and WE1 tanks (89.06% and 82.29%, respectively) than that present in SB2 and WE2 tanks (78.13% and 48.44%, p?<?0.05). The high-throughput sequencing results showed that the diversity of bacterial communities and the abundance of bacteria related to the nitrogen cycle and the degradation of organic matter were increased. The present study showed that H. pluvialis had positive effects on shrimp culture in using artificial substrate system and water exchange system.