As the most abundant phytoplankton in the marine environment, Prochlorococcus plays a vital role in driving element cycle and energy flow of marine ecosystem. Numerous studies indicate that the growth and photosynthetic activity of Prochlorococcus are vulnerable to environmental stresses, thus resulting in the damage to marine ecosystem stability. Therefore, it is crucial to study the responses of Prochlorococcus to environmental stresses for maintaining the marine ecological stability. Generally, Prochlorococcus could adapt to different light and nutrient conditions in the ocean by differentiating into different ecotypes. However, they cannot cope with sudden changes in the marine environment. Here, we review the progress on the responses of Prochlorococcus at physiological and molecular level to environmental stresses, which includes the important role of cyclic electron transport around photosystem I in light changes, RNA-regulated gene expression, and the protection Prochlorococcus against oxidative stress by heterotrophic bacteria. Moreover, we discuss the future directions for studies on Prochlorococcus responding to environmental stresses, aiming to provide fundamental bases to further explore anti-stress mechanisms of Prochlorococcus.