The respiratory tract and digestive tract serve as the gateway between the host and the environment, playing an important role in protecting against viral infections. Diseases caused by viruses that infiltrate the respiratory and gastrointestinal tracts account for the major infectious diseases in pigs, resulting in significant economic losses for the swine industry. However, studies on virus-host interactions are limited due to the lack of suitable research models that can effectively stimulate the highly complex physiological characteristics found in vivo. With the advancement in stem cell technology, organoids that more closely recapitulate the structure, function, and organization of specific organs or tissues in vitro have gradually become a research hotspot. These novel ex vivo models are critical for studying viral infection, investigating viral pathogenesis, elucidating virus-host interactions and developing preventive and therapeutic approaches. Currently, respiratory organoids and intestinal organoids (IOs) have been widely applied in the study of infectious diseases. Therefore, this review primarily summarizes the development of porcine respiratory and intestinal organoids, their applications in studying infection, current limitations, and future perspectives.