The present work reports the interaction of morpholinium based ionic liquid with the transporter protein, human serum album (HSA). The ionic liquids with morpholinium cationic groups are reported to be comparatively less toxic than other cationic groups of the ionic liquids such as imidazolium, pyridinium, piperidinium, pyrrolidinium etc. This work highlight the effect of N‐butyl‐N‐methyl‐morpholinium bromide, [Mor1,4][Br] ionic liquid on the structural stability of HSA. The effect was analyzed by using fluorescence, time resolved fluorescence, UV‐visible, CD spectroscopic techniques and molecular docking method. The results show that [Mor1,4][Br] binds with HSA through weak interactions in which hydrogen bonding and van der Waals forces play major role. [Mor1,4][Br] has a binding site on HSA and binds in the hydrophobic pocket of subdomain IIA of HSA. It was observed that [Mor1,4][Br] retain native conformation of HSA upto certain concentration range. This study endows new insight for designing of such type of non‐toxic ILs that augments their protein stabilizing nature.