The invention relates to a halogen-free flame-retardant polycarbonate composition and a preparation method thereof, and belongs to the technical field of flame retarding. Phosphorus-containing oligomer silsesquioxane with a cage-shaped, trapezoidal or random cross-linking structure is used as a flame retardant to retard the PC. The method comprises the following steps of: mixing polycarbonate, phosphorus-containing oligomer silsesquioxane, anti-melting drop and antioxidant, and then melting, mixing, extruding, cooling, granulating and drying the mixture through a double-screw extruder to obtain halogen-free flame-retardant polycarbonate composition granules. The structural general formula of the phosphorus-containing cage-shaped, trapezoidal or random cross-linking oligomer silsesquioxaneis Tn(OH)m, wherein T=RSiO1.5-m/2n, and R is R1, R2 or R3 or any combination of the three. The adopted phosphorus-containing oligomer silsesquioxane with the cage-shaped, trapezoidal or random cross-linking structure, serving as the flame retardant, has strong flame-retardant property and good thermal stability, so the obtained polycarbonate composition has higher thermal deformation temperature,good flame-retardant property and good mechanical property without containing the halogen.