The invention discloses a screening method of a methylated protective strain for expressing restriction endonuclease FspI. The screening method comprises the following steps: constructing a recombinant expression strain of methyltransferase M.Hhal by obtaining a methyltransferase M.Hhal gene, screening methylated protective strains, obtaining a restriction endonuclease FspI gene, and constructinga recombinant expression strain of the restriction endonuclease FspI; restraining recombinant expression of the FspI, and obtaining a recombinant expression strain of the restriction endonuclease FspI. The method disclosed by the invention realizes efficient recombinant expression of the restriction endonuclease FspI; a lactose operon expression system is used for recombinant expression of the restriction endonuclease FspI; enzyme digestion of a host genome by the restriction endonuclease FspI is resisted; compared with a methylated protection-free expression system, the screening method can stably and efficiently realize the recombinant expression of the restriction endonuclease FspI; the screened methylated protective strain of M.Hhal can be applied to recombinant expressions of other restriction enzymes having similar identification sites as well.