Inflammation is a non-specific kind of biological immune response of body tissues to any type of external or internal injuries, such as pathogens, irritants and immune stress reactions. There are two types of inflammation, namely acute and chronic. Acute inflammation starts and develops rapidly, and is aroused by various factors, including injuries, infection, toxins or immune reactions. Chronic inflammation usually lasts for an extended long period of time and results from elimination failure of acute inflammation, autoimmune disorders, various pathogens and pathogenic environments. Except for the damage itself, there exists a direct and intimate connection between chronic inflammation and various clinic common diseases, such as neurodegeneration, as well as metabolic and cardiovascular ailments. Citrus peel is a by-product generated in citrus juice processing. Polymethoxyflavones (PMFs) exist abundantly and almost exclusively in citrus peels, and their biological activities have been broadly investigated in recent years. PMFs have proven to possess potential inhibitory bioactivities towards a number of functional and immune diseases including inflammation. The two most abundant PMFs exhibiting prominent bioactivities in citrus peels are nobiletin and tangeretin, ubiquitously detected in various citrus species. In this review, the beneficial health effects and the underlying molecular mechanisms of ten main citrus PMFs were illustrated against numerous inflammatory diseases, including inflammatory bowel disease (IBD), neuroinflammation and organ inflammation, among others.