The invention discloses a flame retardant containing silicon and spiro pentaerythritol amyl phosphonate and a preparation method thereof. The flame retardant is characterized in that the name of the compound is a polycondensate of 3,9-dichloro-2,4,8,10-tetraoxa-3,9-diphosphaspiro[5,5]undecane-3,9-dioxygen (SPDPC for short) and diphenyl silanediol. The preparation method of the flame retardant comprises the following steps of: weighing the diphenyl silanedio and the SPDPC according to mol ratio of 1:2.0; weighing an acid aiding agent according to the mol ratio of the diphenyl silanedio to the acid aiding agent being 1:(1.0-3.0); dispersing and dissolving the SPDP in acetonitrile as a diluting solvent; adding the diphenyl silanedio in the mixed solution, mixing and reacting at the temperature of 60-120DEG C for 6-24 hours; cooling the reacted material to room temperature; pouring the reacted material in precipitation reagent deionized water of which the mass is 1-3 times of the mass of the reacted material for precipitating and filtering; and washing with acetone and drying to obtain a white solid flame retardant product with favorable performance.