The invention discloses a method for preparing SSZ‑39 molecular sieves by using fluorine-modified Y-type molecular sieves as raw materials. Y-type molecular sieve is impregnated with fluorine-containing aqueous solution, dried, and roasted to obtain fluorine-doped Y-type molecular sieve; mix and stir deionized water, alkali source, template agent, and silicon source according to the ratio, and add the above-mentioned fluorine-doped Y-type molecular sieve. Sol: transfer the sol to a crystallization kettle, after the crystallization is complete, the crystallized product is filtered, washed, dried, ion-exchanged, and then roasted to prepare a hydrogen-type SSZ‑39 molecular sieve. The present invention modifies the raw material of Y-type molecular sieve by fluorine doping method, so that it can completely transform crystal to prepare SSZ-39 molecular sieve in a relatively short period of time under the condition of relatively low silicon-aluminum ratio, so that the raw material and Cost of production. The SSZ-39 molecular sieve prepared by the invention has the characteristics of short crystallization time, high crystallinity, controllable grain size, good grain dispersion, etc., and can be applied to the fields of methanol-to-olefin reaction, carrier of selective catalytic reduction catalyst, and the like.