Understanding the effect of thermal treatment on the physical and chemical properties of protein and its mechanisms has important theoretical implications in food science. Pea seed ferritin (PSF) is an iron storage protein naturally occurring in pea seeds, which represents a promising iron supplement. However, how thermal processing affects the structure and function of PSF remains unknown. In this work, during the production of pea seed milk, we investigated the effect of thermal treatments at boiling temperature for two different times (5 and 10 min), respectively, on the structure and function of PSF. The results demonstrated that thermal treatment resulted in a pronounced change in the primary, secondary, and tertiary structure, iron content, and iron oxidation activity of PSF. However, the shell-like structure of PSF can be kept during the processing of pea seed milk. Interestingly, upon thermal treatment, both thermal-treated samples exhibit larger higher iron absorption rate by Caco-2 than untreated PSF at the same protein concentration. Such an investigation provides a better understanding of the relationship between the structure and function of food protein, as affected by thermal treatment.