Emodin (EMO), an anthraquinone derivative from roots and leaves of various plants, has been widely used in many inflammatory diseases. Alveolar macrophages (AMs) play a critical role in maintaining alveolar homeostasis in the lung. However, the comprehensive mechanisms of EMO therapy on AMs during acute pancreatitis-associated lung injury (AP-ALI) have not been reported. Both in vivo [caerulein/ lipopolysaccharides (LPS)-induced AP-ALI in mice] and in vitro MH-S models were generated to assess the protective features of EMO on mitochondrial damage and mitophagy dysfunction of AMs during AP-ALI progression. First, in vivo, the relative quantity of AMs was significantly decreased with time in AP-ALI mice; however, the mitochondrial flux presented earlier changes than the relative quantity of AMs in our experimental system. EMO pretreatment significantly alleviated the severity of lung injury and improved the damaged alveolar structure, reversing mitochondrial impairment in AMs. Secondly, in vitro, EMO significantly enhanced mitophagy and alleviated mitochondrial damage. Furthermore, the results following mitophagy inhibition by 3-methyladenine (3-MA) demonstrated that the protective effects of EMO were partially achieved by manipulating the mitophagy-mitochondria-alveolar macrophage axis. These data enabled a more comprehensive understanding of the therapeutic effects of EMO in AP-ALI.