The invention discloses a fish habitat comprehensive protection system for the upper stream, down stream, main stream and branch stream of a reservoir. The fish habitat comprehensive protection system comprises a reservoir upstream main stream fish habitat protection system, a reservoir upstream branch stream fish habitat protection system, a reservoir downstream branch stream fish habitat protection system and a reservoir downstream branch stream fish habitat protection system. The reservoir upstream main stream fish habitat protection system is arranged at the position, above a reservoir dam, of a riverway main stream. The reservoir upstream branch stream fish habitat protection system is arranged at the position, above the reservoir dam, of a riverway branch stream. The reservoir downstream main stream fish habitat protection system is arranged at the position, below the reservoir dam, of the riverway main stream. The reservoir downstream branch stream fish habitat protection system is arranged at the position, below the reservoir dam, of the riverway branch stream. According to the fish habitat comprehensive protection system, the overall healthy and sustainable development need of the ecological environment of the upper stream, down stream, main stream and branch stream of the reservoir is met, the river fish habitat protection theoretic and technical study system in China is filled and perfected, and social benefits, economic benefits and environmental benefits are all achieved.