The invention relates to a fluorine-containing alpha-oxo ketene dithioacetal compound as well as a preparation and an application thereof, the structural formula of the compound is shown in the figure, wherein, R1 is fluorinated chain C1-C4 alkyl; R2 is hydrogen atom, halogen atom or the like; R3 is C1-C6 hydrocarbyl, benzyl or aromatic group; R4 is C1-C6 hydrocarbyl, benzyl or aromatic group; The preparation includes: using fluorine-containing aldehydes compound as raw material, in the presence of alkalis, executing a substitution reaction for the material with carbon bisulfide and haloalkane in an organic solvent medium by a one cooker method, and then removing dissolvent, eluting residues by a silica gel column chromatography and collecting product. The alpha-oxo ketene dithioacetal compound can be used as building block in organic synthesis with wide applications; and the invention has the advantages of simple and convenient preparation method, great adjustability of structure, lowcost, environmental friendly and good economic benefit.