Abstract: Lonicera japonica, a traditional medicinal plant in China, is rich in various bioactive compounds such as organic acids, flavonoids, iridoids, and triterpenoid saponins. It exhibits multiple pharmacological effects, including broad-spectrum antimicrobial, antiviral, anti-inflammatory, immunomodulatory, and antioxidant activities. In human medicine, L. japonica has been widely used for preventing and treating respiratory infections, inflammatory diseases, and viral diseases. The direct antiviral mechanisms (such as inhibiting neuraminidase activity and blocking viral replication) and immunoregulatory functions of its core active components (e.g., chlorogenic acid, flavonoids) have been extensively studied. In recent years, with the increasing intensification and scaling of the livestock and poultry industry, frequent outbreaks of viral diseases such as avian influenza, Newcastle disease, and porcine reproductive and respiratory syndrome (PRRS) have posed continuous threats to the industry. At the same time, issues caused by antibiotic overuse including drug resistance, drug residues, and environmental pollution have become increasingly severe. There is an urgent need to develop safe, efficient, and sustainable green antibiotic-alternative strategies for disease prevention and control. In this context, L. japonica and its extracts have gradually gained widespread attention for their potential application in veterinary clinical practice and healthy farming, owing to their multi-component, multi-target, low-toxicity, and residue-free characteristics. This review systematically summarizes recent advances in the use of major bioactive compounds from L. japonica for the prevention and control of viral diseases in livestock and poultry. It elaborates on the remarkable effects of organic acids such as chlorogenic acid and flavonoids such as luteoloside, which operate through multiple mechanisms. These include direct action on viral particles, interference with viral adsorption and entry, inhibition of viral replication, and modulation of host innate and specific immune responses. These mechanisms contribute to the control of important viral diseases such as avian influenza, Newcastle disease, PRRS, porcine circovirus disease, and bovine viral diarrhea. Beyond its core antiviral role, this article also discusses the value of its broad-spectrum antibacterial activity in controlling secondary bacterial infections following viral disease, and analyzes the synergistic effects of its anti-inflammatory and antioxidant properties in alleviating virus-induced tissue damage and promoting organism recovery. This review aims to provide a reference for the development of novel green veterinary drugs.