Insulin bound with ligand molecules can improve its bioavailability in oral formulations. In this work, the interactions between insulin and bile acids of taurocholic acid (TCA) and glycocholic acid (GCA) are characterized using different mass spectrometry (MS) methods. Electrospray (ESI)-MS analysis revealed that GCA and TCA could interact with insulin individually or together through non-covalent bonds, and the products included mGCA-insulin, nTCA-insulin, and mGCA-nTCA-insulin complexes. Their binding stoichiometry, relative intensity ratio (IRa), and binding affinity were determined. ESI-MS/MS data and the calculated association constants both suggest that TCA has stronger affinity to insulin than GCA. The mixtures of various insulin, GCA, and TCA complexes with different charge states were separated, and distinct trend lines were observed using ion mobility mass spectrometry (IMMS). Moreover, liposomes containing insulin and GCA and/or TCA were prepared, and directly characterized using ESI-MS, and the interaction products of insulin with GCA and TCA were found in the liposome formulation. AutoDock was used to simulate molecular binding and select binding sites between insulin and GCA or TCA to explore the interaction mechanisms. The findings in this work could help understand the mechanism of action of insulin protection with bile acids in the body.