The invention discloses clean drilling fluid used for a coal bed gas multi-branch horizontal well storage layer and a preparation method of the clean drilling fluid. The drilling fluid consists of the following materials in parts by weight: 100 parts of clear water, 0.5-1 part of a gelatinizing agent, 0.5-1 part of gelatinizing aid, and 0.1-0.2 part of a high temperature stabilizer, wherein the gelatinizing agent is composed of hexadecyl trimethyl ammonium bromide and cetyl pyridinium chloride monohydrate in a weight ratio of 4:1; the gelatinizing aid is composed of sodium salicylate and potassium chloride in a weight ratio of 1:1; the high temperature stabilizer is sodium thiosulfate. The drilling liquid does not use bentonite or polymer to improve viscosity, but uses micromolecule surfactant to form a micelle for increasing viscosity, is good in rock carrying capacity, quick and complete to break glue, and capable of guaranteeing a well hole to be clean while protecting the coal bed gas storage layer to the greatest extent, and reducing scouring of drilling fluid on well wall, so that drill blocking risks are lowered, and therefore, contradiction between the drilling safety and the storage layer protection in a drilling process of the existing coal bed gas multi-branch horizontal well is relieved to a certain extent.