Marine resources are rich in biologically active substances including lipids, carotenoids, polyphenols, etc., and are widely used in food, medical, and other industries. Microwave-assisted extraction (MAE), as an efficient, green advanced extraction technology, exhibits better heating efficiency and less energy consumption than traditional extraction methods. As a promising wet lipid extraction process, the extraction efficiency of MAE is mainly depended on the operating parameters and the types of raw materials. The extraction of carotenoids by the MAE method is mainly focused on the extraction of astaxanthin, fucoxanthin, and β-carotene. In addition, MAE has been widely studied for the extraction of other biologically active substances such as polyphenols and phycobiliproteins. The joint use of MAE and other extraction technologies is also widely applied and has great potential. This chapter focuses on the applications and trends of MAE to extract important compounds (i.e., lipids, carotenoids, polyphenol, phycobiliprotein) from marine resources.