The invention discloses a porous concrete waterproofing agent and a preparation method thereof. The waterproofing agent is prepared from, by weight, 25-40 parts of modified gel, 4-6 parts of an oxidizing agent, 5-9 parts of a cross-linking agent and 3-5 parts of a photoinitiator; the modified gel is prepared from, by weight, 30-40 parts of pretreated microspheres, 25-30 parts of 3,4-dihydroxyphenylacetic acid, 15-20 parts of N-hydroxysuccinimide, 15-20 parts of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride, 18-25 parts of sodium alginate and 10-14 parts of propyne. According to the porous concrete waterproofing agent and he preparation method thereof, process design is simple, and component proportion is reasonable; chitosan and sodium alginate are modified, and a Michael addition reaction and a chemical click reaction are used for forming a compact double-gel network, so the waterproof and seepage-proof performance of concrete can be effectively improved in use, meanwhile, the waterproofing agent can be self-repaired, and the waterproofing agent can be widely applied to concrete construction and has high practicability.