We identified 6 hub genes (IL1R1, CD163, TLR5, LY96, MMP9, and IRAK3) and 4 target miRNAs (miR-34a-5p, miR-103-3p, miR-107, and miR-124-3p) that affect the pathophysiological processes of T2DM and CS through ion transport, immune response, and infection. Here, MMP9 is linked to infection.