The commercial cationic surfactants (CSAa) with quaternary ammonium (QA) groups have proved to be broad-spectrum bactericide against bacteria, fungi, and viruses. Nevertheless, they inevitably exhibit potent irritation on the skin. In this work, we systematically investigated the regulatory mechanism of the host-guest supramolecular conformation with β-cyclodextrin (β-CD) on the bactericidal performance and skin irritation of CSAa with different head groups and chain lengths. When the ratio of incorporated β-CD is not greater than 1:1, the bactericidal efficiency of [email protected]β-CD (n > 12) remained above 90 % due to the free QA groups and hydrophobic fraction that can act on negatively charged bacterial membranes. And once the ratio of β-CD exceeded 1:1, the β-CD attracted to the bacterial surface by hydrogen bonding might prevent [email protected]β-CD from acting on bacteria, resulting in a decrement in antibacterial performance. Even so, the antibacterial activity of CSAa with long alkyl chains (n = 16, 18) was independent from the complexation of β-CD. Accordingly, both the zein solubilization assay and the neutrophil migration assay on zebrafish skin evidenced that β-CD attenuated the interaction of surfactant with skin model proteins and the inflammatory effect on zebrafish, thereby enhancing skin mildness. In this way, we hope to create a simple but effective brainpower using the host-guest approach to guarantee both bactericidal efficiency and skin mildness without modifying the chemical structure of these commercial biocides.