In recent years, many viruses that are associated with human infectious diseases have been detected in healthy bats, including the Rabies virus, Ebola virus (EBoV), Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Unlike other mammals, bats do not appear to show overt clinical signs of infection. Therefore, people can learn new knowledge to fight against the viruses by studying the immune system in bats. Here we review recent studies on innate immune system in bats, and highlight the unique charateristics of their innate immunity. Among all mammalian groups, bats are the only group capable of flight, which may have led to a suite of unique antiviral response mechanisms in bats. Meanwhile, bats have evolved novel mechanisms to limit virus-induced inflammatory responses. Notably, bats have a rich species diversity with more than 1400 species across the globe, which accounts for more than 20% of all mammal species. We call for in-depth studies on the diversity of immune genes in bats, which would facilitate a deep understanding of the unique immune functions in bats. Together, learning from bats about their immune systems would be fundamentally important for humans to control infectious diseases and develop animal husbandry.