The invention discloses a safe, environmental-protection and high-efficiency silicon wafer cleaning agent comprising the raw materials: N-methyl-pyrrolidone, anhydrous sodium carbonate, sodium metasilicate, a Dynol604 surfactant, a Surfnol465 surfactant, a Surfnol104 surfactant, a low-foaming surfactant, fatty alcohol polyoxyethylene ether, nonylphenol polyoxyethylene, dihydroxyethyl-trihydroxymethyl imine methane, nitrilotriacetic acid, OP-10, sodium dodecyl benzene sulfonate, sodium diethylhexyl sulfosuccinate, hexafluoropentanedione, beta-diketone, Twain 80, triethanolamine, quaternary ammonium base, diethylene glycol monomethyl ether, ethylene glycol monomethyl ether and deionized water. The invention also provides a preparation method of the safe, environmental-protection and high-efficiency silicon wafer cleaning agent. The silicon wafer cleaning agent has the advantages of good cleaning effect, high safety, environmental protection and no pollution.