Heat-trapping of atmospheric high CO2 causes global warming, a censorious parameter that leaves an antagonistic impression on all photosynthetic organisms’ physiological and productive activities. To reduce these high CO2 levels, the Carbon Concentration Mechanism (CCM)-based microalgal CO2 mitigation was considered the most efficient non-negative impact method. The photosynthetic regulatory mechanism of all photoautotrophs is the primary target for high temperatures, resulting in decreased photosynthesis and productivity rate. Therefore, to counteract high-temperature stress on productivity, it is necessary to understand the high-temperature acclimation responses of CCM and the photosynthetic network in the cell at the molecular level. This will provide great insight into how photosynthetic light and CCM genes network together toward high temperatures for stable photosynthesis. It also increases the concern over developing thermotolerant strains. This review goes through some of the molecular responses of the microalgae Chlamydomonas reinharditii, a plant model, to high temperatures. It discusses how the organism senses heat, initiates protective mechanisms, and alters the expression of genes related to carbon concentration mechanisms and photosynthesis to acquire thermotolerance.