Photosynthesis is a vital metabolic process that transforms light energy into chemical energy, producing oxygen and organic compounds essential for the survival of almost all life forms. Photosynthesis is coordinated by unique lipids, photosynthetic protein complexes, and their associated cofactors and pigments within thylakoid membranes. Molecular dynamics (MD) simulations complement experimental techniques, offering a powerful tool for probing the intricate details of thylakoid membrane dynamics, lipid–protein interactions, and the impact of environmental conditions on photosynthesis. In this chapter, we have extensively discussed recent MD studies focusing on the dynamical behaviors of both simple and complex lipid mixtures representative of thylakoid membranes. The chapter highlights the importance of MD simulations in understanding the impacts of lipid composition and environmental factors, such as temperature and dehydration, on structural integrity, phase properties, and lipid–protein interactions of the photosynthetic membranes across various oxygenic organisms. The detailed molecular insights derived from computational studies thus may assist in developing improved strategies for the sustainable cultivation of marine macroalgae or seaweeds under varying environmental conditions.