The invention relates to a hydrophobic granule and a preparation method thereof, and a waterproof breathable structure and a forming method thereof. The hydrophobic granule comprises aggregate and a hydrophobic resin film coated on the aggregate, wherein the aggregate size is 6-300 meshes, and the hydrophobic resin film is made of one or a plurality of hydrophobic epoxy resin, bakelite, polyurethane resin and silicone resin, and coated on the aggregate. The preparation method of the hydrophobic granule comprises the following steps: heating the aggregate to 50-400 DEG C; adding the hydrophobic resin, evenly stirring so that a film is coated on the aggregate surface; and cooling, crushing and screening to obtain the hydrophobic granules. The hydrophobic granule can be widely used as a waterproof breathable layer in desert planting, lake bottom seepage-proofing, river course seepage-proofing, landscape water system bottom seepage-proofing, and has favorable waterproof and breathable properties.