The invention discloses a hydrothermal synthesis method of a Fe-MFI molecular sieve. The method comprises the steps of (1) fully mixing an iron source, a silicon source, a template agent and deionizedwater, performing hydrolyzing, and keeping the temperature at 60-90 DEG C to obtain molecular sieve precursor gel; (2) preparing a crystallizing auxiliary agent, wherein the crystallizing auxiliary agent is CeO2-RuO2 composite oxide powder; (3) mixing the molecular sieve precursor gel with the crystallizing auxiliary agent, placing the mixture in a sealed vessel for heating to 160-180 DEG C, preserving the heat for 3 days or above, and then performing filtering, washing, drying and roasting to obtain the Fe-MFI molecular sieve. The hydrothermal synthesis method of the iron-containing MFI molecular sieve is improved, the catalytic conversion rate of the prepared iron-containing MFI molecular sieve on alpha-phenylethanol is obviously increased, and the catalytic stability of the synthesizedFe-MFI molecular sieve is superior to that of a Fe-MFI molecular sieve synthesized by means of a common synthesis method.