The invention discloses a method for preparing recombinant phycocyanobilin, in particular a method for producing the recombinant phycocyanobilin by gene engineering technology. The method comprises the following steps of: cloning phycocyanobilin synthesizing key enzyme genes (hol and pcyA) from algae and cloning the key enzyme genes to proper expression vectors; inoculating a recombinant vector into an Escherichia coli expression system for heterogenous expression, and synthesizing the recombinant phycocyanobilin through enzymatic catalytic reaction; and finally performing extraction, chromatography and other purification steps to prepare the recombinant phycocyanobilin. The prepared recombinant phycocyanobilin has the advantages of higher capacity of removing DPPH radicals, can be used for treating a plurality of diseases caused by oxidative damage, and also can be used as an additive in functional foods.