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All eight pangolin species, especially captive <i>Manis pentadactyla</i>, are critically endangered and susceptible to various pathogenic microorganisms, causing mass mortality. They are involved in the complement system, iron transport system, and inflammatory factors. <i>M. pentadactyla</i> exhibited a higher abundance of opportunistic pathogens, <i>Moraxella</i>, which potentially evaded complement-mediated immune response by reducing C5 levels and counteracting detrimental effects through transferrin neutralization. In addition, we found that the major structure of C5a, an important inflammatory factor, was lacking in <i>M. javanica</i>. In brief, this study revealed the differences in immune factors and microbiome between <i>M. javanica</i> and <i>M. pentadactyla</i>, thus providing a theoretical basis for subsequent immunotherapy.