Infectious diseases impose global challenges to public health. Infectious diseases can be caused by various pathogens, such as bacteria, parasites, fungi, or viruses. Over 1 million people worldwide die from viruses such as HIV, hepatitis C or B virus (HCV or HBV) in 2016. Recent outbreaks of Zika, Ebola and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) bring serious threats to global health security. On account of the high probability of an unpredictable virus pandemic, there is an urgent need for broad-spectrum antiviral drugs. Herbal medicine (HM) is a valuable source for the treatment of infectious diseases. A conventional traditional Chinese medicine (TCM) treatise ‘Shanghan Zabing Lun’, which recorded over 200 herbal formulae (known as Zhongjing’s formulae), also known in English as the ‘Treatise on Cold Damage Diseases’ has a history of around 1800 years. However, these ancient TCM formulae and theories are rarely used in nowadays methodologies for developing curative from HB. In this perspective review, we summarize the ancient theory of herbal medicine for treating infectious diseases including flu and malaria. The novel strategies for developing novel anti-infection drugs by modern integrated techniques for example, knowledge mining, high-content screening, phenotypic assays are also discussed, which will shed light on revealing novel properties and biological functions of phytochemicals inspired by ancient medical knowledge.