The invention relates to the field of water-based drilling fluids, in particular to modified polyhistidine applicable as a supermolecular shale inhibitor, a preparation method thereof and applicationof the modified polyhistidine in water-based drilling fluids. A histidine polymerization main chain of the modified polyhistidine has a structural unit shown as the formula (1) and connected with a modifying group and has histidine polymerization degree of 6-9. The modified polyhistidine provided herein is a degradable biomaterial, having good environmental friendliness; when applied as a shale inhibitor, the modified polyhistidine with its supermolecular character is effective in inhibiting hydration swelling of the leading swellable mineral montmorillonite in shale, and has excellent inhibitory effect and high temperature resistance.