The invention discloses an organic silicon electronic packaging material and a preparation method thereof. The organic silicon electronic packaging material comprises methyl-terminated polydimethylsiloxane, a plasticizer, an inorganic filler, an organic filler, a flame-retardant assistant, a functional assistant, a crosslinking agent, a catalyst and an exempt volatile organic solvent. The preparation method comprises the following steps: uniformly dispersing the polydimethylsiloxane and organic filler by high-speed stirring and mixing; previously carrying out high-temperature baking on the inorganic filler, adding, dispersing by stirring, adding the plasticizer, and uniformly dispersing by high-speed stirring; adding the flame-retardant assistant and bonding assistant, dispersing by high-speed stirring, dispersing, adding the crosslinking agent, dispersing, adding the catalyst, dispersing by low-speed stirring, adding the solvent to regulate the viscosity, continuing dispersing, vacuumizing, and discharging to obtain the product. The organic silicon electronic packaging material has favorable bonding performance for PC (polycarbonate), PTFE (polytetrafluoroethylene), stainless steel and aluminum products. By using the exempt volatile organic solvent for preparation, the organic silicon electronic packaging material is green and safe, and has the advantages of favorable storage stability, favorable temperature tolerance and excellent electric properties.