The invention discloses a methyl silicate stone protecting agent and a manufacturing method thereof. The methyl silicate stone protecting agent comprises a methyl silicate, at least one type of silane coupling agent, at least one type of polyethylene glycol and at least one type of water, wherein the adding amount of the methyl silicate is 8-20% of the total weight of a polymer; the adding amount of the silane coupling agent is 1-5% of the total weight of the polymer; the adding amount of the polyethylene glycol is 0-5% of the total weight of the polymer; and the adding amount of the water is 70-91% of the total weight of the polymer. The manufacturing method disclosed by the invention comprises the following steps: dissolving the polyethylene glycol in a small amount of hot water according to the proportion, then sequentially adding sodium methyl silicate and the silane coupling agent in a stirring state and finally replenishing water till 100%. The methyl silicate stone protecting agent disclosed by the invention has the advantages of waterborne and environment-friendly properties, no toxicity, no volatilization, no pollution, short curing time, stable chemical performances, simplicity, convenience and flexibility in construction and operation, safety and low cost. The methyl silicate stone protecting agent is suitable for waterproofness and moisture-proofness of various natural stones, artificial stones and the like. The methyl silicate stone protecting agent particularly has an excellent waterproof effect on the stones with relatively large holes, such as sandstone, cavity stone and the like, and can simultaneously prevent affecting the air permeability of the stones.