Bee pollen is a mixture of pollen, nectar, and bee saliva. It is rich in bioactive substances, including polysaccharides, flavonoids, carbohydrates, proteins, vitamins, and minerals, conferring high nutritional and pharmacological value. The flavonoids in bee pollen are considered the main components responsible for its active function. Based on a systematic elaboration of the physicochemical properties and classification of bee pollen flavonoids, this review summarizes the preclinical research progress of bee pollen flavonoids in inflammation-related diseases, with a focus on prostatitis, colitis, and neuroinflammation, and analyzes the key bottlenecks limiting their application. It should be noted that the current evidence is primarily derived from pharmacological studies at the cellular and animal levels, and the clinical efficacy in human diseases has not yet been confirmed; their potential effects are mainly established on the basis of biological plausibility and preclinical potential. This review aims to provide a reference for subsequent fundamental research and translational exploration of bee pollen flavonoids and to offer insights for the design of future clinical trials.