The invention discloses a preparation method of a flexible silica aerogel, relating to a silica aerogel. The invention provides the preparation method of the flexible silica aerogel, which takes methyl alkoxy-series silane as a silicon source precursor. The preparation method comprises the steps of mixing methyl trimethoxysilane or methyl trimethoxysilane, an anhydrous ethanol solution and water, further adding hydrochloric acid, regulating the pH value of the solution to 2-2.5, then adding ammonia water to obtain a sol, standing, then preparing a wet gel, further aging the wet gel, and then drying to prepare the flexible silica aerogel. The prepared flexible silica aerogel has the advantages of low density and high porosity, and simultaneously overcomes the shortcomings of poor integrity and great brittleness. According to the preparation method, the complicated steps of complex solvent exchange and gel modification are not required, so that the operation is simple and easy, the process is controllable, the cost is low, the period is short, and the continuous production can be realized.