Ocean acidification (OA) affects macromolecules of marine organisms by affecting acid-base balance, energy metabolism, cellular stress response, macromolecular transportation and gene expression, while the composition and contents of the macromolecules play a decisive role on the existence, growth and development of marine organism. Up to now, seldom reports are on this field and the mechanism of OA effects has not been cleared. The present paper reviews the studies on the effects and mechanisms of OA on marine biological nucleic acids, proteins and fatty acids which, provides a basic information for the control of OA at the molecular level, and provides reference for the protection of marine ecological environment and organisms as well as scientific regulation of aquaculture seawater.